You will probably have to use two different Windows user accounts for their particular iPod. I don't think you could have two different accounts on the same Windows user account.
And each account to there account/iPod, as well. This may be tricky, but can be worked out. But two user windows user accounts is probably a necessity in this kind of thing.
By the way, do you have two iPods, or are you just wanting to have two different iTunes accounts?