Since VideoMonkey is using ffmpeg to do conversion, you can have ffmpeg mux in a second audio track while encoding. It just takes an extra couple of lines at the end of your normal conversion feed. It works properly with tagging, too, unlike the old hybrid MooV files VisualHub created.
ffmpeg -i <input> <your conversion flags here> output.m4v -acodec copy -newaudio
On a non-surround video file, you'll end up with two stereo tracks, so it would probably be best simply to limit this behavior to files with >2 channels.
This is reason I have postponed using Video Monkey.
Call me non-observant, but I extremely annoyingly converted half of my AVI library with VM before I realised I had detrimented the original 5.1 sound to just a stereo output :-(