beedish,
You never want your source unit to access power from a different battery than the amplifiers. The same current flow created by voltage potential attempting to circumvent the dual battery isolation and equalize, that causes the noise, can indeed harm the fragile IC OP amps that are the preamp output of your source unit. It is precisely the ground shield on the RCAs that pass the voltage even though they may terminate into 10kOhms. I'm sorry for getting technical but I've got to give you what is really taking place and the risk involved.
If you properly wire the Perko switch so that all the stereo equipment including amplification, the helm buss and the starter/alternator cable is connected to the Perko common post and nothing else is wired directly to the batteries except the Perko switch #1 and 2 posts, then you will never have to worry about the above noise or possible equipment failure.
Moving the source unit ground and/or supply off the factory harness is always a good idea, especially as your system gets more sophisticated. Connecting them to the primary terminals of your largest amplifier satisfies the need to reference the lowest potential difference at the most critical relationship.
ACR/VSRs can, not always, but can get more complex. Many totally isolate all stereo equipment on one battery while combining the house bank/helm buss and alternator feed/starter on the other bank...especially when using a really large stereo. However, some models of boats will dictate other schemes. But since you are not looking at that option right now I'll let it pass.

David
Earmark Marine