how to charge 2 batteries in a captiva 192

My boat mechenic told me I did not have to remove the batteries and keep them on a charger as I have always done in the past. When I go to raise the stern drive to keep it higher the batteries do not seem strong enough to raise it. I have a battery charger that worked for the past two years on these batteries. The boat has a selection switch to select the batteries or a setting for both. Do I have to charge each battery one at a time or is there a way to charge both batteries at once if the selection switch is set to both. I was thinking on placing the positive clamp from the charger on battery one and the negative clamp on battery 2.