From everything I can tell this is an install error. If you have minor hiss with the PDX you need a line driver/pre amp, that is pretty self explanatory. But what you are talking about is flat out weird because from what I can tell your subs are the only ones being driven by the amp...???
Post specific pics showing what wires were tapped into, the connections, your ground etc. That would probably help more than anything.
There is also a possibility that you fried somethign in HU from a short, in which case the CDA may be your best bet.