The choice depends on how long you are willing to wait for enough batter charge to go out after finding out that you left something turned on after the last visit. In simple terms, the 36 amp is going to charge up the depleted batteries in half the time that it would take the 20 amp Are the four batteries set up with two banks of 2 batteries in parallel or are the batteries set up with ACRs or some other 'smart charge controller connected to the motors charge circuits