You might want to look into what is called an ACR - Automatic Charging Relay. Lots of people make them. I personally like the Blue Sea Systems brand.
My boat has a starting battery for each engine, and a two-battery house bank. The house bank is on it's own ON-OFF switch. Each engine has it's own OFF-1-2-ALL switch. I can combine each engine on both starting batteries if needed.
With the ACR, each engine is wired through the ACR to the house bank. This isolates the house batteries from feeding back to the starting batteries; however, when the starting batteries are fully charged, the ACR starts putting the charge to the house batteries.