Is your iTunes currently signed into his account instead of yours?
I'm just making a guesses and this does not solve your immediate problem, maybe create a user account on your Mac for him, so when he logs into his computer user accuont, he can then login to his own iTunes account and all your own stuff will be left alone within yours.
If you use the same iTunes account, you can do it just by ensiring that the devices have different names. Then just go to the various panes (Apps, music etc.) and check the boxes so that only selected items sync to the iPod.