Not quite understanding what you are trying to accomplish. I would urge you to go to "Blue Seas" website for wiring diagrams (
https://www.bluesea.com/). A telephone call to them will get you exactly what you need.
You should also reference:
https://www.outbackmarine.com.au/ass...m%20Design.pdf
I believe the problem with your solution is that if the main switch is off, then the batteries will not charge because the
current from the engine/alternator charge will be stopped at the switch. But that could also apply to the genset too if the
generator runs off the same bank.
Your other issue appears to be that you do not want current from the alternator to blow the controller or voltage
regulator from another charging source, hence the need both an isolator and controller.
You also are not going to want one batter to draw down the other to the point that you cannot turn over your
generator or engine, so again, you are going to need some form of isolator between the batteries to stop one battery from discharging the other.
I hope this helps because I really don't quite understand what you are attempting to achieve. The On-Off-Both switch should be used to disconnect ALL current being drawn in the
boat. It should not be used to control a charging system.
In my
boat, the chargers bypass the switch so that ALL of the batteries are always receiving a charge from one source or another, no matter if the battery switch is set to 1, 2, or both.