There are a number of ways to do this, but I think the easiest thing to do would be to simply create a standard playlist for either of you (or two for both of you respectively), and just drag your respective music to each playlist. So, for example, create a playlist called "Jim's music" and drag all your music into that. That way, all the music will be available in the Library source, but you can simply use that playlist to automatically filter out her music.
If you wanted to make this automatic, you'd have to throw some work behind it, but you could go edit multiple songs' information such as putting your name(s) in the Groupings or Comments section, and then creating a Smart Playlist and using that criteria to have it automatically generate the proper playlists (if you know any scripting, you could create a script to do this for you, such as AppleScript if you have a Mac). Any new imported music would just have to have its song information edited, and it'll be automatically added to the proper Smart Playlist(s).
In any case, the next time you fill up your iPod, you should have an option at the bottom of the iTunes' main window when you select the iPod in the Source pane that also allows you to Autofill from the desired playlist(s) and source(s), provided the iPod supports the feature.
I would strongly advise against unchecking any songs, as you have to do this on a per song basis.
