I should not be changing the load and therefore should not have a diode problem.

That has always been my habit as that was how I learned to sail.

As soon as the engine is off, I can and do switch.

As far as charging I have a shore power charger that has two separate channels and runs separately to each battery with an inline fuse within about a foot of the battery. That charger is on it's own AC breaker separate from the AC outlets on the boat. I normally keep the AC off on the boat, but run the charger all the time while connected to shorepower.

I believe I have a galvanic isolator (but I plan to test for proper installation... just got some Nigal Calder data on how to do so) I do not at this time have a combiner, nor a good way to test SOC of my batteries. I have an ampmeter in line and a voltmeter, but both are analog and installed by the boat builder... and leave something to be desired. The ampmeter for instance is too highly scaled for my typical use of under 15 amps... this barely registers on the meter.