Many ways to go, and your (new) way should meet your needs.
But consider the possibility that this system might end up with the same music file on your drive AND her drive, using extra disk space. And if you look at the entire library you'll see it as duplicates -- and hear it as duplicates if you play the entire library. Not a big deal for just a few tracks, but maybe you'll have many tracks in common?
Another approach is to put everything on one drive, even in one folder structure, then use a custom field (or a certain value in a standard field) to identify what you like, and what she likes, and what you both like. I use the multi-value Keywords field, and have all kinds of keywords, for music style, in some cases music purpose ("dinner"), vintage, etc. It's then easy to create smartlists that filter on whatever combination of Keywords and other fields I choose -- part of MC's power is to have MANY playlists, for many purposes, all based on one library.
I do this with my iPod and my wife's iPod -- different musical tastes. We each have our own smartlist that we sync to our iPod, but from the same library/tracks, so if we both end up with a track, because we both like it (maybe for different reasons, as specified by multiple keywords), it's coming from the same ONE track on the library drive -- very efficient to store, update, etc.
Having everything in one place is disk-efficient and makes it easy to create backups.