ETAF,
You have options available to you.
1. different instances of Firefly running with different config files to separate the music
2. Playlists made by iTunes to separate the music
3. FireFly smart playlists to separate the music.
4. More, probably but am not thinking of any.
If you setup your genre tags on your music 3 is the easiest way to go. If not 2 is pretty good as well. I have never done 1 and so can not comment.
Craig