As Caleb said, I would home run each speaker pair back to the amplifier to connect to each channel of the amplifier. Within each room locate a good spot for a volume control and terminate the 4 conductor from the amp there, and then run (2) two-conductor wires from that volume control location to the speakers in the room.
One bit of advice, run a CAT5 cable along with your speaker cable, even if you decide not to do any muting/paging/IR stuff. It will allow you, or a future owner, to add control down the road without a HUGE hassle.
I prefer the Audioplex Technology stuff, they have some cool home paging through existing speaker stuff. Check out this link for some muting options like the niles, and then this link for the cool paging system through the speakers. Feel free to ask me more questions on this (in private if you desire), I have a lot of experience with these devices.
EDIT: Just noticed this was a couple months old...sorry.