if its a whining noise then its more than likely comming from the alternator, you would get it if your head unit was working propoely with the amps, the interference is comming down the power cables from the battery, you can either put a supressor on the alternator, change the alternator, or change the power cables, you should only have 1 cable comming from the battery, the split it close to the amps, that minimises noise from the engine bay, check the route that the cables take from the battery to the cabbin, make sure it goes no where near the alternator or any other mechanical part, ( i know it and egning but see if you can get the cables as far away as poss for most of the engine.
the other possibility is its gear box whine, i had it but thats cos i put the RCA's near the grear box, a quick and easy test is run the RCA's from the head unit out side your car and to the amp that way, then you can tell if it is gear box or alternator.
is your car front wheeled drive or rear wheeled drive, cos if its rear you could be getting noise from your Diff. try the RCA out of the car thing first though