The USB drive and DCIM folder on it are only for copying photos (taken or saved) from the iPad to your computer. It behaves pretty much the same way a camera would. Like a camera, it's not recommended you delete photos from the iPad using the computer's file manager.
To do more you either need to download and use iTunes 11, or use a combination of third party apps for the iPad and computer. The third party solutions are too numerous and media specific for me to go into. If you decide you don't want to use iTunes (and some people do not) then you can ask or search for each thing (music, photos, etc) that you want to accomplish.
After you install iTunes, but before you connect the iPad:
Click on the on the iTunes Store button on the right (if you are in Library mode) and sign in with your Apple ID. In the Store menu choose Authorize this Computer.
Now plug in your iPad.
Since you have been using your iPad for a while, the first thing iTunes is going to want to to is help you re-initialize it. I doubt you'll want to do that. The initial dialog when you plug the iPad in will probably give you the option to Erase or Transfer Purchases. Chose the second. If it does not offer you the Transfer Purchases option cancel the dialog and go to the View Menu to enable the Sidebar (if it isn't already visible). Find your iPad under the Devices list in the sidebar, right click it, and choose Transfer Purchases.
This can take quite a while, depending on how much iStore content you have on the iPad.
After the transfer is done, go through all your sync settings and make them the way you want. Pay close attention to the App section and make sure all your apps have checkmarks next to them. If they don't, they will be de-installed on your next sync.
To get a better idea of how to use iTunes (and other good info) get the
iPad User Guide from either
Apple's site or in the
iBooks Store. Both are free.
