Make an embedded 5.1 QT

I have a prores movie in FCP. I've mixed a 5.1 soundtrack in soundtrack pro and imported the discreet tracks back to FCP.
Now I'd like to make a H.264 movie that will play from Plex (which I guess is the same as saying play from Quicktime?) as a movie with 5.1 sound in the same way as one of my files I have ripped from DVD using handbrake plays.
I can see ways to make two separate files but not one embedded file. I'd also like to keep the frame size 1080.
I've tried exporting a self contained movie to see if handbrake can open it and export it but handbrake wouldn't open it. Is there a way to do this in FCP Studio?

I'm just a FCE user. But what I do is using QT Pro for joining video and 5.1 tracks. Than I import the .mov files in iTunes. At this moment QT(7.6.2) lost ability for Dolby surround 5.1 playback with perian. iTunes still can, because Apple wants to sell their movies from the store.
Completely confusing situation.
I'm doing this with QT because FCE can not handle 5.1 files.
BTW, are the 5.1 files you wish to import AIF, Dolby or AAC tracks?
For Dolby 5.1 you have to use Compressor to turn AIF 6 track files into Dolby 5.1

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Case:
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Do

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