There seems to be some confusion on how to do this. Twice today people asked how to do it because they keep overwriting the photos on their iPad. So here is the proper way to do it. If you still can't figure it out after this guide, you should probably just set your iPad on fire or send it to me because it's really not that complicated. 
First things first - let's understand how iTunes syncs your photos.
1. Once you pick folders to sync, iTunes will detect changes in those folders and sync your iPad accordingly. So if you have a folder called Photos with 35 wedding photos in it, and then decide to erase those from your hard drive and replace them with 42 photos from your last vacation, when you sync with iTunes it is going to look at that folder, see that you made changes, and sync with your iPad. So it's going to delete the 35 wedding photos from your iPad and replace them with the 42 vacation photos. Also, if I alter those photos, for example, go in and eliminate red eyes from a picture and save to the same file name...iTunes will detect that you made a change to that photo, and DELETE the red eye photo from your iPad and replace it with the corrected one. If you do not save it as the same file name, iTunes will detect a new photo and ADD it to the collection of other photos from that folder already on your iPad.
2. iTunes cannot distinguish between sub folders. So that means if you have a folder called photos (let's say c:\Photos) with a bunch of sub folders...say Wedding, Cars, Vacation, and so on. And you simply select to sync all photos from c:\Photos it is going to put them all in one place. So all of your porn is going to be mixed with your baptism photos. If you manually sync these folders (screen shot to come) and check the individual sub folders of the main folder you are syncing, iTunes will put them into separate folders on your iPad.
NOTE: If you have subfolders within subfolders, such as c:\Photos\Wedding\Ceremony and c:\Photos\Wedding\Dances all of the photos from the Ceremony and Dances folders will be sync'd into ONE folder on your iPad called Wedding. Unfortunately, there is NO way around this. If you want to separate the folders mentioned above, you would have to make subfolders called c:\Photos\Wedding Dances and c:\Photos\Wedding Ceremony to get them into separate folders on your iPad, which is what I did.
3. You CANNOT delete your photos once they are sync'd to the iPad if you plan to sync your iPad again in the future. So if you have a folder called c:\Photos, and you are auto downloading your photos from your digicam into that folder, and it auto creates a folder called like c:\Photos\2010-06-05...if you DELETE that folder called 2010-06-05 and all the photos, and then sync again, iTunes will recognize that folder is no longer in your library and will REMOVE any photos that were previously contained in that folder from your iPad. Once your photos are on the iPad or on iTunes, that does not mean you can delete them!!!! If you delete them, iTunes will delete them from your iPad the next time you sync that folder!
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Ok, now we start the sync process.
If you notice in the screenshot below, you will see how I have my folder hierarchy set up in Windows Vista. I actually have a dedicated external 2TB hard drive to manage all of my iPad photos and videos. The two video folders are TV Shows and Movies, the rest are filled with photos related to the title of the folder. So the folder entitled Afghanistan are pictures from my deployment to Afghanistan whilst the folder entitled Addie are pictures of our dog. The iPod photo cache is something iTunes creates, just leave it be.
You could do it the same way except just make a folder on your hard drive called iPad instead, or you could do it the way I do it to keep things a little more organized.
So after you decide how you're going to set up your folders on your computer for storing your photos, you're going to plug in your iPad and start up iTunes.
Once you do that, your iPad should appear in the pane to the left. Mine is called Matthew's iPad. Once that shows up, click on that. That will bring up your sync area.
Next thing you want to do after you've clicked the name of your iPad, is in the right pane, click on the tab entitled "Photos". It should be near the far right, mine is the last tab.
You should now see a check box and "Sync Photos From...". Make sure the check box has a check in it, and then click on the gray drop down box and choose "Choose Folder". This will bring up a browse style window, like you see below.
What you want to do next, is find the folder or hard drive you created for storing your iPad photos. In my case it is an external hard drive called iPad, so it's pretty easy to find. If in your case, you created a photo folder called c:\Photos with subfolders like c:\Photos\Wedding, c:\Photos\Cars, etc...then you want to select the folder entitled c:\Photos or whatever your root folder for your photos is. So you would have to navigate to the drive C:\ and then double click the folder Photos (in this example).
When you double click that folder in the browse window to select it you will see the contents of that folder like below (notice how the contents of this folder match the contents of the expanded hard drive you saw in the first screen shot):
From here DO NOT navigate any further into the folders. Notice I have a ton of sub folders but I am not going to select any of them. Simply hit the "Select Folder" button in the dialog box.
Now you will be taken to this screen:
NOTE: If you choose "All Folders" radio button at the top, ALL, and I mean ALL of the photos contained in the root folder and ALL of its sub folders will potentially be stuffed into ONE giant folder on your iPad like I discussed at the beginning. The easiest way to have control over what gets sync'd when and how is to choose the "Selected Folders" radio button and put a check mark next to each individual folder you want to sync.
Next hit sync and let iTunes run it's magic. iTunes will create a folder on your iPad for every check box you have checked from the screen shot above.
In the future, REMEMBER: say I change the contents, on my computer (not my iPad) of the folder above called Afghanistan (you can see it in the screen shot as being selected for sync)...ANY CHANGES I MAKE to that folder on my computer, will reflect on my iPad when I sync that folder. So if I delete all but one photo from the Afghanistan folder on my computer, when I sync that folder to my iPad, ALL BUT ONE PHOTO will be REMOVED. If you change the contents of the folder, like replace all the photos from Afghanistan with wedding photos, when I sync that folder to my iPad ALL OF THE AFGHANISTAN PHOTOS WILL BE REMOVED AND REPLACED WITH WEDDING PHOTOS. In addition, say for example I have three subfolders under Afghanistan. iTunes shoves the contents of all three subfolders into one folder called Afghanistan on your iPad. If I delete an entire subfolder from my hard drive, iTunes will delete the photos contained within that subfolder but not the folder Afghanistan from your iPad. The same goes for adding a subfolder with new photos.
First things first - let's understand how iTunes syncs your photos.
1. Once you pick folders to sync, iTunes will detect changes in those folders and sync your iPad accordingly. So if you have a folder called Photos with 35 wedding photos in it, and then decide to erase those from your hard drive and replace them with 42 photos from your last vacation, when you sync with iTunes it is going to look at that folder, see that you made changes, and sync with your iPad. So it's going to delete the 35 wedding photos from your iPad and replace them with the 42 vacation photos. Also, if I alter those photos, for example, go in and eliminate red eyes from a picture and save to the same file name...iTunes will detect that you made a change to that photo, and DELETE the red eye photo from your iPad and replace it with the corrected one. If you do not save it as the same file name, iTunes will detect a new photo and ADD it to the collection of other photos from that folder already on your iPad.
2. iTunes cannot distinguish between sub folders. So that means if you have a folder called photos (let's say c:\Photos) with a bunch of sub folders...say Wedding, Cars, Vacation, and so on. And you simply select to sync all photos from c:\Photos it is going to put them all in one place. So all of your porn is going to be mixed with your baptism photos. If you manually sync these folders (screen shot to come) and check the individual sub folders of the main folder you are syncing, iTunes will put them into separate folders on your iPad.
NOTE: If you have subfolders within subfolders, such as c:\Photos\Wedding\Ceremony and c:\Photos\Wedding\Dances all of the photos from the Ceremony and Dances folders will be sync'd into ONE folder on your iPad called Wedding. Unfortunately, there is NO way around this. If you want to separate the folders mentioned above, you would have to make subfolders called c:\Photos\Wedding Dances and c:\Photos\Wedding Ceremony to get them into separate folders on your iPad, which is what I did.
3. You CANNOT delete your photos once they are sync'd to the iPad if you plan to sync your iPad again in the future. So if you have a folder called c:\Photos, and you are auto downloading your photos from your digicam into that folder, and it auto creates a folder called like c:\Photos\2010-06-05...if you DELETE that folder called 2010-06-05 and all the photos, and then sync again, iTunes will recognize that folder is no longer in your library and will REMOVE any photos that were previously contained in that folder from your iPad. Once your photos are on the iPad or on iTunes, that does not mean you can delete them!!!! If you delete them, iTunes will delete them from your iPad the next time you sync that folder!
************************
Ok, now we start the sync process.
If you notice in the screenshot below, you will see how I have my folder hierarchy set up in Windows Vista. I actually have a dedicated external 2TB hard drive to manage all of my iPad photos and videos. The two video folders are TV Shows and Movies, the rest are filled with photos related to the title of the folder. So the folder entitled Afghanistan are pictures from my deployment to Afghanistan whilst the folder entitled Addie are pictures of our dog. The iPod photo cache is something iTunes creates, just leave it be.
You could do it the same way except just make a folder on your hard drive called iPad instead, or you could do it the way I do it to keep things a little more organized.
So after you decide how you're going to set up your folders on your computer for storing your photos, you're going to plug in your iPad and start up iTunes.
Once you do that, your iPad should appear in the pane to the left. Mine is called Matthew's iPad. Once that shows up, click on that. That will bring up your sync area.
Next thing you want to do after you've clicked the name of your iPad, is in the right pane, click on the tab entitled "Photos". It should be near the far right, mine is the last tab.
You should now see a check box and "Sync Photos From...". Make sure the check box has a check in it, and then click on the gray drop down box and choose "Choose Folder". This will bring up a browse style window, like you see below.
What you want to do next, is find the folder or hard drive you created for storing your iPad photos. In my case it is an external hard drive called iPad, so it's pretty easy to find. If in your case, you created a photo folder called c:\Photos with subfolders like c:\Photos\Wedding, c:\Photos\Cars, etc...then you want to select the folder entitled c:\Photos or whatever your root folder for your photos is. So you would have to navigate to the drive C:\ and then double click the folder Photos (in this example).
When you double click that folder in the browse window to select it you will see the contents of that folder like below (notice how the contents of this folder match the contents of the expanded hard drive you saw in the first screen shot):
From here DO NOT navigate any further into the folders. Notice I have a ton of sub folders but I am not going to select any of them. Simply hit the "Select Folder" button in the dialog box.
Now you will be taken to this screen:
NOTE: If you choose "All Folders" radio button at the top, ALL, and I mean ALL of the photos contained in the root folder and ALL of its sub folders will potentially be stuffed into ONE giant folder on your iPad like I discussed at the beginning. The easiest way to have control over what gets sync'd when and how is to choose the "Selected Folders" radio button and put a check mark next to each individual folder you want to sync.
Next hit sync and let iTunes run it's magic. iTunes will create a folder on your iPad for every check box you have checked from the screen shot above.
In the future, REMEMBER: say I change the contents, on my computer (not my iPad) of the folder above called Afghanistan (you can see it in the screen shot as being selected for sync)...ANY CHANGES I MAKE to that folder on my computer, will reflect on my iPad when I sync that folder. So if I delete all but one photo from the Afghanistan folder on my computer, when I sync that folder to my iPad, ALL BUT ONE PHOTO will be REMOVED. If you change the contents of the folder, like replace all the photos from Afghanistan with wedding photos, when I sync that folder to my iPad ALL OF THE AFGHANISTAN PHOTOS WILL BE REMOVED AND REPLACED WITH WEDDING PHOTOS. In addition, say for example I have three subfolders under Afghanistan. iTunes shoves the contents of all three subfolders into one folder called Afghanistan on your iPad. If I delete an entire subfolder from my hard drive, iTunes will delete the photos contained within that subfolder but not the folder Afghanistan from your iPad. The same goes for adding a subfolder with new photos.
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