Some detail about the system you have would be useful. As said above alternator whine is induced because of a grounding issue of some sort, either the earth on the amp or the HU, if this is poor then you get a disparity between the earth at the HU and at the amp and this is what causes the interference as a tiny current will flow through the screen on the RCA's. It can also be poor quality RCA cables or poor quality amp. It won't be anything to do with the speakers or speaker wiring.