Yes, you would have to put a switch in the ground side of the second batteries ground path. Otherwise there would be a short for the first battery in the 24 volt system. As long as you are only charging the batteries the 37amp Alternator will produce enough current. It would not though produce enough if you tried to use the trolling motor while running the engine. This would be unusual though. I have wired many series-parallel systems on different units over the years which only had low current generators. If you have many other consumers the current requirements will be greater. It would help to know if the charging system on the big engine is on an inboard or an outboard. Increasing the charging system capacity is very easy on an inboard, but no so easy on an outboard.