Question about alt whine.

Hey guys, I was wondering if alternator whine will harm my subwoofer? Right now I hear it in my speakers and when the subwoofer is installed I know it will be producing this noise also. Will the noise harm the sub?

It can depending on how harsh the noise is, and the frequency its playing at. You need to fix the problem before installing a sub, you are either picking it up through the rca's, or you need to find a better ground point.