it is possible for a capacitor to reduce or eliminate engine whine... but like he said, look for other possible causes first before spending money. In an audio system, the capacitor is normally used to help with sudden current draws from the amp, reducing strain on the cars charging system.

Check your grounds, if you have more than one amp, make sure they are all grounded to the same point. If your RCA cables are run on the same side of the car as your power wire, try seperating them.