The 'normal' way these work is that the selected battery is used/charged. The unselected battery is disconected completely. If you choose 'BOTH' (or 1+2) on the battery switch, then both batteries are being charged (or discharged). It's easy to check these things with a voltmeter, but if you're not sure, get someone that knows what they are doing check it out for you.
Unless you have a dual battery charger, then both of the batteries may be charged when you are on AC power.
Or if you have dual engines, some things may be wired differently ( one battery per engine, so that each will charge when the respective engine is running.
My 1990 Maxum was sold today. I had it less than one year, but it was good to me!