You can, but you need to manually Sync instead of letting it automatically sync. Then you just need to manually move the songs you want onto the iPod.
It is a bit of a pain because it takes longer, but we do that because DH has a lot of crap on his that I don't want on mine.
All your songs will be on iTunes, I don't know of a way to have seperate iTunes for each iPod.
When you connect the iPod to your computer, you should get a summary type page. In the "Options" portion check "Manually Manage Music".
You'll probably want to reset his iPod and start over. Select "Restore" on the summary page. It'll wipe everything off the iPod.
To move music onto the iPod, you can just drag from your iTunes library and drop onto the iPod (listed under Devices).