Wow, there are a lot of settings we could play with in iTunesPrefs.plist inside the /Media folder!
Somehow, and I'm still trying to figure it out, I was able to get my music inside appleTV's main "menu" without it getting copied to the media folder (and creating 2 copies of all my music on my hard drive). I don't know how I did it, because usually enabling syncing made 2 copies, but this time it didn't duplicate the files and I can access all the music from appleTV without going into the sources menu! (iTunes still has to be running) There are some settings in the .plist like "automaticMusicUpdate" and "homeMusicDatabaseID" which might be useful... Also, I noticed a few settings were different when I compared the .plist I had backed up before getting this to work and after. We might be able to specify where to look for media...