IPad – How to download .ipa files to iTunes/Mobile Applications during sync

For the first question, I think its actually stored under C:\Users\username\My Music\iTunes\iTunes Media\, if everything is standard. If anything, it will be wherever your music is also stored (just in another directory).

As for your second question, I don't think you can tell it not to sync the apps. The only ways to not keep them would be to delete off your iPad before sync, or delete from the file system after sync.

You can back up as many iDevices to your computer as you please (technically). On my computer, I sync and have backed up at least three different iDevices.

All you need to do, is plug in your iPod Touch to your laptop, open iTunes, and back it up. It will know the difference between your iPod touch and iPad.

The difference comes in if you sync music from a computer (but that isn't relavent to this question, so I won't elaborate).