What is the best way to be able to control a 5.1 surround system with 2 seperate Zones. Are there any 3 zone receivers like that or would I be better off getting a receiver for the 5.1 surround and a seperate 2 zone receiver for the other rooms?
There are indeed 3 zone receivers. One good example which I had the opportunity to review recently is the Denon AVR-3313CI. It can be had for a reasonable price - but it does depend on your budget. What are you looking to spend? There are offerings from other manufacturers, but I believe the Denon to be a great solution with many good features including solid remote control apps, air play, and dual HDMI output.
I don't really have a budget. I'll pay what it takes to build a good system. I had a house built and its almost done. All the pre-wire is done. I didn't want to pay the builders contractor's ridiculous price so I just had them pre-wire. I've heard that other zones will require an amp to power them?
I would like to have surround sound from the TV and the other 2 rooms running separate audio for the both.
You'll need a stereo amp for the 3rd zone, but with the Denon that should cover you. If you want 7.1 in the media room at any point, then you'd need a 2nd 2 channel amp for zone 2 instead of using the surround back channels.
For a 2 channel amp, you can go from something as simple and affordable as this: http://www.parts-express.com/pe/showdetl.cfm?partnumber=300-383
Or, something more "serious": http://www.crutchfield.com/p_580M282/Onkyo-M-282.html?tp=180&kw=&org=pla&nw=g&crv=6488474185
There are a plethora of options. Many people also try a pro-sound amp: http://www.bhphotovideo.com/bnh/controller/home?O=&sku=790562&Q=&is=REG&A=details
I'd use the Onkyo personally, as it's just a great deal and a good solid performer.