How Do I Charge, and Maintain 2 New 6 Volt Batteries???

You need to break out that new multimeter and start measuring your charger's output. That would put a lot of your fears at rest. After you have the batteries installed and when you have the shore power on, measure at the battery posts for voltage. Since you have a fully charged bank, voltage from the converter should be 13.2 --->13.6 volts.