H20,

Since the noise is present on all the speakers, its safe to say its generated at the source and feeding both amp. Is it present with the tuner and CDs as well?

Yes, by all means, the head-unit needs to have its yellow B+/MEM and black GND need to be terminated to the same battery source as the amps. Good news is, this will not effect how you are turning on your head-unit currently with the switch on the dash. This function is actually done by a small red wire on the head-unit that is fed B+ through that switch.

So, by your post, im gathering your boat only has a single battery. If so, then I would not rewire anything just yet as the whole system has no choice but to share the same battery. I would inspect the RCA cables connections real close. A loose RCA can induce some static type noise. Next, I would inspect the B+ and GND connections and any crimps/splices along thier path. If any are suspicious, then just rerun them directly to one of your amps. I did this same thing today on a Baja that had a head-unit powering down while the boat was under way. The feed came from the transom off the battery, and had 3 splices within a foot of the head-unit. Cut them all out and went directly to the tower amp that was 18" away and fed by 4ga cabling.

One means of isolating the issue is to take a 3.5mm headphone jack x RCA and go directly from your MP3 to each amp. If the problem goes away, then you know its upstream on the source signal.