The way I have seen it done is you purchase a zone controler that plugs into the AC unit and Heat Pump. Then you plug your thermostats and or temperature sensors into the controler. I have seen a few from smarthome.com (http://www.smarthome.com/prodindex.asp?catid=412
They also offer dampners that can shut off the AC or heat to certain rooms or locations. You can plug each rooms sensor into the one controler and then plug the dampners into the controler. Then control each room individualy or the whole house.
I think they are mostly controled through RS-232/485.
Smarthome offers a lot of various solutions for any size project. I have recently been turned on to Insteon and am waiting for Pluto to add support to thier system. Good luck.