if you use the Apple TV preset, it should do a pass through track of the 5.1 sound automatically.
I wonder how many people (I'm one) are converting the video for play on Apple TV, XBOX, PlayStation, etc. would it be worth (in another thread) working out a good compromise for settings and creating one h264 video for these players and uploading it somewhere? The risk I guess is diluting the official release with too many different versions.