Can two devices be synced on the same computer?

My sister has this old iPod that she wants the songs synced up to her iPhone, and I don't know how to use her computer so I'll use mine. The thing is, my iPhone is already synced to it… However, if it is a different user account (computer account, not iTunes) what will happen? Can I sync it?

Yes, i think so.

More than one device can be synced on the same computer, regardless of whether you have different or the same Windows User Account.

Now, here's where it gets kind of complicated.
If it's separate -where both of you have separate iTunes libraries made possible by Windows User Account- you can simply do a drag-and-drop transfer. Create a user-shared folder -a folder that can be accessed and modified from you and your sister's user account- and drag the songs your sister wants from your iTunes window to that folder.
You can't directly sync your sister's iPhone with your iTunes; you have to use the method that I gave you or another. Otherwise, this would result having your sister's iPhone's data being overwritten and her data being lost. Even if you change the way things are synced to her iPhone, the data that's not present in your iTunes will be the data that's deleted from her iPhone.