Is the netflix app on the TV itself, or on your Directv box? You must have the audio coming from the box, either going through the tv, then to your surround system, or direct to your surround system. Sounds like only one audio line is comming through. For example, if you have optical (or any connection) from your box to your surround system ONLY, when you use your apps on your TV, that will only be outputted through your TV speakers as it is not being fed to your surround system.
Hope this is clear enough, and i have not confused you any further!
Good luck,
Kenton.