Jeremy,
Try this:
Assuming you have an AirPlay compatible H.264 video file with no audio …
Pull your stems into Compressor using the Add Surround Sound Option. Use the AC3 file preset. Use Coding Mode:
3/2 (L,C,R,LS,RS). Enable LFE.
Now have Compressor build the file.
Next use Quicktime 7 to open the H.264 video and the encoded AC3 audio file. Make sure you queue the movie file and the audio file at the beginning. Select the audio file window – from menu:Edit/Select All/Copy.
Now select the movie window – from menu:Edit/Add to Movie
Now check Show Movie Properties from the QT 7 menu. You should see the AC3 audio track with the proper channel routing. Save it out. That should do it …
-paul.