all power wires should be PERPENDICULAR to any signal wires from the head unit to the amp, now this is impossible. somethings you can do is wrap the signal wire with aluminum foil, and separate the signal wires from the power wire where ever possible.
for example, on mine, i ran power down the left side and signal down the right, and where they meet up i tried to cross them perpendicularly,
also, does the whine change with increased throttle? if so thats alternator whine, you may also have a ground loop problem. are all the grounds going to the same spot, and are they well grounded?
have a looksee here:
http://www.mp3car.com/vbulletin/car-...ing-guide.html