Is it correct in that the pop only happens when the stereo is on and you crank the boat? No pop if you turn on the stereo with engine off, or wait to turn it on after the engine is running? The recommendation to run on 1+2 seems like they are chasing a voltage sag.
First have to determine which circuit is falling out of sequence. Is it the IGN turn-on? (may not even be one). Is it the constant B+? Or is it the amps hitting their voltage threshold and cycling off then back on.
Both the ground and B+ share the load equally, so if one needs to be upped, both would, unless one is smaller then the other, which would be odd.
Load, or stress on the charging system is relative to the discharged level. So two batteries can be now more load to the alternator then one battery. Think of audio amplifiers. five 100W amps are in theory, no more of a load then a single 500W amp. Same with batteries.
A large stiffening CAP may "fix" the issue, but they can be a liability to the battery(s) on toys that are not used regularly.