If you disregard losses through the wire, both series and parallel would result in the same amps going to the batteries. Each panel will produce about 9 amps at 31 volts. Parallel totals 18amps x 31volts = 558 watts. Series totals 9amps x 62volts = 558 watts. 558watts / 12volts = 46.5amps to the batteries. Connecting the panels in series will reduce the voltage loss in the wire from the panels to the controller. The result will be more amps delivered to the batteries. How much more will depend on your wire size and length of wire.
