I have a Sea Ray 280 Sundancer with two batteries and a lot of stuff that stays on. You won't create any problem turning through "Both" to the other battery. As a matter of fact, with the engine running (charging), you should NEVER turn the switch through "Off" to the other battery.
They charge best one at a time. The main purpose for the "Both" setting is if batteries are weak and you need help starting. Voltage is the same but it will raise your cranking amps. If out boating or fishing, ride away from home on one battery and back on the other so both will get charged.
