Add a 2 channel track to video file

I have a WD TV Lube Hub media center hooked up to my TV/surround system in the living room, and it's loaded with movies, all in mkv container, DTS or DD 5.1 sound.
I've been using iVI Pro/iFlicks/Road Movie to convert them for iPad, using pass-through video conversion settings so they just convert the audio to AAC 2 channel and leave the video as-is, and re-container it. Very quick, and works a treat.
Problem is, it means I end up with 2 copies of the same movie on the drive (1 with a DTS/DD 5.1 audio track, 1 with a 2 channel AAC audio track).
Is there any of simply inserting the 2 channel AAC track into the existing movie file so it'll play on iPad?
I don't want to simply use the AAC 2 channel version of the movie for everything and delete the other one, because if I decide to watch the movie on the TV in the living room I then won't have DTS/DD 5.1 surround sound.

I agree with Karsten.
What I would do in this case would be to create the first movie in iMovie. Then use FILE/DUPLICATE to create a duplicate of the project. I would then add the second audio track to this duplicate.
You could either mute the original audio track so you just hear the commentary, or you could use the ducking feature so that you can hear the original track at a softer volume while hearing the commentary track at full volume.
You would then need to share both projects to iTunes. You would have two distinct movies on your TV.
Here is a good video tutorial for how audio works in iMovie.

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    From: [email protected]
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