I've had no problems with alternator whine on the speakers. I tried to keep the power running down the drivers side and all audio cables runnin down the center or passenger side.
My Auzentech audio card has the 3.5mm audio jacks for center, sub, rear and front speakers. To connect them I bought a cable long enough to reach the amps, with a 3.5mm end and an RCA connection to the amp. sort of like this.