I guess I just don't understand iTunes. I have downloaded several apps directly to my iPad over wireless. I connected the iPad to my PC and watched it perform (a) a backup, and (b) said it was syncing and then complete. The apps on my iPad are now not showing up in iTunes. I assume I want them to show up in case I need to do a restore or something.
If I select Sync in iTunes it only seems like it is going to push the few in iTunes to the iPad. I want the ones from my iPad to go back to iTunes, right?