So, we have eliminated the two file setting in the camera. Now, let's talk about the Photo app, this app comes with your iPad. Across the top in the app, there are four sections Photos, Albums, Events, Places.
Press Photos, you get every single photo on the iPad.
If you press Albums, you get the Albums you created with a sync from a MAC/PC Source AND your camera. All of the photos you import from your camera will be in the album: All Imported.
Press Events, you get just the photos that you imported from your camera organized per session--there should be several folders that are sequentially ordered 100import, 101import, etc. (I don't use geotagging for my photos, I do not have any working experience of "places" but I've seen it in action on other friend's iPads that use this geo-tagging extensively.)
HPulmer indicated that if you continue to use the same memory card to import more files, the iPad will also add already imported files. Any file that already exists on the iPad, would be renamed with a (#). This is the logic used when you get the choice of deleting photos once imported.
(Managing your photos with your iPad is very simplistic and doesn't give you the kind of flexibility you will need as your portofolio grows, for example, whatever name your camera creates to name a file, will be imported to the iPad in that same file name. You can't rename it to something that would be more descriptive of the content.)
When you say you have photos in three places and if you were to delete them in one part of the app, it is also deleted in other folders--that is because you only have one copy of the file. I hope this helps you get a better idea how this app works.