"Alternator whine" can come from many places: induced into the signal chain via the RCA cables, into the circuit via a ground loop problem, through the factory harness, etc. You need to troubleshoot and find out what's causing the problem. Bypass your entire signal chain by running an (RCA) output from a small boombox/radio to your amplifiers and see if the problem persists. If it does remain, your problem is not in the signal chain, but most likely in the wiring. If the problem goes away, you know its somewhere in that signal chain. Bypass each component individually (one at a time) including cables, until the problem goes away. Obviously this tell your the piece causing the problems. Dont forget, your headunit itself may be picking up noise via the factory wiring harness. In any serious system or one with potential noise probs, I always run a seperate ground and power wire for the headunit over from the fuse panel (and closest ground point). This bypasses the factory dash harness for the setreo completely.
I would not recommned a 'noise filter' as they are simply a bandaide for the real problem. There is no reason you cannot build a noise-less system without bandaids in your ride, people do it every day.
Running power and ground wires close to each other is perfectly fine, its the RCA cables carrying your signal that should be placed as far from the power and ground cables as possible, as current passing through the wire creates a magnetic field that can induce noise into the signal chain. A recent theory however is that it does not matter, because in a chassis ground the 'return' side of the circuit is the car itself, and keeping your wires far from that is well... impossible. The situation is a bit more complex than that and Im not 100% sure about that theory, but its a possibility. My point? If you are worried thats the problem (noise induced into the cables), bypass them by running another RCA outside your car (temporary) from the deck to the amps, and see if the problem goes away. If your problem is induced noise in the cables, it would go away at that point. But I doubt that's your problem honestly, as it sounds like a more acute problem. I suspect its a ground loop problem with the amps, or noise in the factory harness.
Few ideas to get you heading in the right direction.