I'm no electrical guru
but from your diagram, your # 2 battery (the one on the right), would only charge when the switch is on 2 or both. (unless you missed labeling an 'off' option in which case only the number 1 (left) battery would charge) Is that what you want?Also when your outboard is running, it will only charge both batteries, if both are selected with your switch. Otherwise, again, only your nuber 1 will charge.If your switch has an off function, and that is selected while you are away from the boat, then only your number 1 battery will charge.I cannot comment on your alternator question, because I don't know. My suggestion would be to have your solar charger + and - go directly to the charge controller + and - respectively as you do now, and then to the + and - of each battery bypassing the 1 2 both switch. This way, both batteries will charge from the solar panel, even when your switch is off, and thereby cutting current to anything else on your boat, including your motor.As I read your diagram, your whole boat's electrical system is live, whenever you are charging with the solar panel, because you have to have at least one or both batteries selected to have them charging. Your outboard is live as well, ready for someone to push the start switch and off with your boat.