Voltage-wise it doesn't make a difference, you get 12 Volts either way. The two 12 Volt batteries wired in parallel will allow a tad more current than the two 6's in series due to the internal resistance of the batteries. If there is plenty of room in the battery compartment, go for the 12's. Here's a web site with lots of info:
LeeH
(published on 05/28/2010)
