For me, the best way to handle is it to either
1) Have two playlists, one for each iPod, and have just that playlist sync. You can have just that playlist sync by clicking on your iPod when it is plugged in on the sidebar, then clicking the music tab, and then you can check off only certain playlists. I am pretty sure that's how you do it but I am doing it from memory.
2) Manually sync (it sounds like you are...)
I have never tried this method, but I imagine it works: create seperate user accounts ON THE COMPUTER for each person. Not sure if you are on a Mac or PC but if its a PC, then go to Start -> Control Panel (make sure you are in "Classic View") -> User Accounts, and then add a new one from there. This should work since iTunes files are stored in the "My Music" folder for each different user, so if you have different user accounts the music should stay seperate.
As I said I have never tried that method but I am 98% sure it would work. Not to mention I found it on Apple's site. Apple has other ways that should work (including my playlist idea), so if you want you can go check it out:
http://support.apple.com/kb/HT1495
However, I highly reccomend trying that last method since it would probably be easiest and would allow both users access to ALL features on iTunes. Good luck!