You can run multiple ipods with separate selections.
If you are using a single library then you should set a playlist(s) for each device.
When you sync the device then on the left menu click the ipod under Device. Go to Music select Selected Playlists, artists etc. Point the playlist or artist selections underneath to your wife's playlist selection(s)
To use each persons i`tunes account sign in by clicking the account detail shown top right if the chosen account needs changing