Does the whine vary when you rev the engine?

I'd first check your sub amp's ground. Make sure it's tight, and if it is, try moving it. Then I'd check your rca's, try disconnecting one channel at a time and see if it still whines. Then try swapping the rca wires completely. If none of that works, it could easily be the amp itself, the rca ouput deal on amps is shit most of the time.