It's probably easier if he has his own account with the iTunes store unless you don't mind him downloading (charging) your iTunes account for things he wants. Regardless of which way you go, you can each sync only the applications/songs, etc... you want because iTunes will see each device as a separate device and allow different syncing preferences.
FYI- You posted in the iPod Touch forum, but you mentioned iPad in your question. Same principles apply though.
Apple's support website has a lot of good information about how iTunes works as well. Take a look there and you should be able to find what you need.