Let me save u guys some pain: you won't get what you want...certainly not an "all in one" or remotely painless process, anyway. I beat a bunch of poor people to their electronic deaths looking for such a reality.
Well, certainly not while instituting apple tvs/ios devices, anyway.
I would suggest simply utilizing something inexpensive and versatile- like the WDTV Lives- for the non-primary rooms. You can then continue ripping mkvs and they'll playback in every room.
As an Apple TV, iPad, and iPhone user I can assure you that I REALLY wanted to have the best of both worlds, but it simply cannot be done without a LOT of extra time and space. Instead, I'll have EVERYTHING in every room and simply transcode the stuff I MUST have for the pads and phones.
Contrary to what others believe, one day the movie world will be "iTuned" by apple and it will operate much like music collections do today (across devices, everywhere) and this will all be over...but I'm not betting it's gonna happen in the next couple years.
Actual phone call (see pic to left):
Tech (responding to laughter): "I'm sorry sir, did I miss something?"
Me: "Yeah, a case of Diet Mountain Dew walking across my living room."