We need more info. It sounds like a definite bad ground, but then you say if you tinker with one of the amps, it stops. Perhaps the ground connection IN THE AMP is bad?
Meh, some solder will solve that pretty quick. If you think it's the amp, disconnect the amp, right the speakers some other way, if you lose the whine, it's the amp.
However, a 90 amp alternator isn't going to get you very far, especially when bi-amping. I worry mine might die on me. I never play music in my car more than 5-10 minutes without the engine running. I killed a Diehard Silver 60 month battery that way. Just remember the big 3.