If you have a 5.1 surround system, you want to make use of it. However, you may not always be able to do that when you create your own videos to import to Apple TV. Normally, this may involve ripping a DVD with Handbrake or using tools like Subler for the audio in internet videos.
Ars Technica put together a little how to that helps users set things up.
1) Handbrake is great for ripping DVDs or converting video – Here
2) Subler is a better tool for those who have internet videos and want to convert the audio to something useable on their Apple device – Here
Check out Ars for more details: Ars Technica