Well, I don't know if there's an easier way, but here's what I've done.
I recorded two different versions of the same movie - one with the regular 5.1 audio and one with the commentary.
For the extras, I created a TV show group called Movie Extras, and dumped all the little things (mostly from the kids movies, all 5-10 minutes each) there.
Reasonably organized, but maybe there's a better way?