So after days of hard work I finally succeeded, aside from one last question.
I've used the workflows to rip full backups of my BD/SD DVD's, then ran Handbrake making certain the .m4v's have AC3 5.1/6-channel and AAC layer sound.
I have a new Pioneer VSX-33 that supports 7.1+ AC3/AAC sound. Streaming the m4v's from my Mac Pro via iTunes to my Apple TV 2 produces 5.1 surround sound as indicated on my Pioneer AVR. Here's the rub:
I have my aTV2 connected to a secondary 1TB "Time Capsule" that is configured to extend my wireless network with another "Time Capsule". This "Time Capsule" supplies internet radio via ethernet to my Pioneer VSX-33 and also connects via ethernet to my aTV2. I jailbroke my ATV2 with Seas0nPass, installed XBMC and NitoTV. I then configured XBMC to use the HDD on my "Time Capsule" through SMB. This allows me to copy my m4v's to my "Time Capsules" HDD, which then allows my aTV 2 to play the movies via XBMC.
I have all the parameters in place. AC3, DTS are selected in XBMC and "Digital Audio - AUTO" in Apple TV 2 settings are selected (HDMI is carrying video/audio to my Pioneer AVR). However, I am not getting any indication that the sound is 5.1 through this method, nor does it appear to be as "crisp" as streaming via my Mac Pro in iTunes through Home Sharing. I've read all the XBMC forums (seems this may be an issue), and aside from trying Plex, I'm not certain what I may be doing incorrectly. I really need to get the converted m4v's onto that remote HDD, but if there is no way in maintaining full quality I'll have to settle for home sharing and leaving gig's of movies on my Mac Pro.
Any help would be AMAZINGLY appreciated, as all of you have been extremely helpful in getting me this far. One more step and I'm DONE

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(PS I've had to buy another 2TB HDD for my Mac Pro as I ripped 1.5 TB's of BD/SD's in less than three days thanks to your efforts!)
UPDATE:
"If my first audio track in an m4v is AAC the second AC3 track won't play, other than that everything is running lovely."
Is this confirmed? How is it possible to force AC3 if the first audio track is AAC? Simply by selecting the track order in Handbrake?