beedish,
Seldomly are the proximity of the RCAs to the power wire a real source of noise unless you run them parallel over a long distance. Its more of an accumulative issue with cheaper RCAs, lose RCAs or overgained amplifier inputs. So just avoid long side by side stretches and you should be fine. We've never had to actually move RCAs in a boat. Its a bit different in a car if you run both down the same side under tight rocker panels over a 15 foot span.
Yes, even though the memory circuits don't usually have any relationship to the signal path, while you are at it go ahead and move the memory too. Some people run the memory battery direct so they don't lose programming over short durations but they add a switch for long term storage as to avoid the drain which can empty a battery in 3 to 4 weeks. It depends on the particular radio defaults and your particular usage as to whether or not this is worthwhile.
If you want isolation from the helm buss but you still want the switched function a basic interrupt relay (horn relay from any auto parts store or stereo shop that does alarms) will do the trick. Its very easy surgery.

David
Earmark Marine