I'm not sure exactly what you mean, but, based on what I think you mean, here's my explanation:
If you and your sister use different accounts on your Mac(s), you'll have different iTunes libraries altogether (unless you've jumped through hoops to combine them)... so no worries.
However, I suspect that you both use the same account and so share an iTunes library. In that case, you'll both have access to the same pool of songs, but you could choose to manually select which songs you each want on your iPods. You could create a folder for her songs and one for yours, then use those folders to load your iPods. And there are other things you could do as well to keep the songs "separate" even though they're in the same iTunes library.
Is this even close to what you wanted to know? If you explain your situation a bit better, perhaps I could be of more help.
Edit: your iPods will always have some or all of the iTunes songs in them, but they aren't really "duplicate iTunes" in the sense you implied - iTunes just shows what's on the iPods when they're connected, which, of course, will be copies of what's in the iTunes library. Each iPod might have some of (or all of) the same songs as the other iPod, but that's not a problem.
