Depends
Hi Marcio,It depends on how your charger is wired. On our boat the battery charger is wired directly to the battery terminals, bypassing the switch. Hence it doesn't matter where the switch is set, the charger will replenish all three batteries in our system.The alternator on the other hand is wired through the switch. Consequently, when the engine is running it will only charge the battery (ies) determined by the switch.Following the connections from your charger back to the switch and the batteries should give you the answer. Hope this helps.Gary WyngardenS/V Shibumi H335