noise from speakers

I have a 2006 Ford Fusion. I just put in a Pioneer AvicD3, MTX 9500 series sub, a mono block Thunder Elite Amp, and a 4-channel Thunder Elite amp. I installed the power wire running to the back down the Drivers side, and the RCAs and Speaker wire down the passenger. I have the power and ground running through the distribution block to both amps. I believe I am getting an Alternator Whine, since the noise goes up as I rev the car up. I replaced the RCAs with new ones, and the noise did not go away. If I disconnect the RCAs from the Head Unit the noise is still there. It goes away as soon as I disconnect the RCas from the amp. I have even tried a new amp to help the problem. What do you thinkI can do to help this out? All help is greatly appreciated.

The engine noise is very loud. If I have the key in the on position, but the car is not running the noise is there. If I use the delay turn off on my car, and take the key out, the noise is gone.

Just for clarification... Are you saying that when the car is running and you take the key out using the delay turn-off, the whine goes away, but if you put the key in with the car NOT running, there is a whine?