Unfortunately I'm getting ready to head to bed so I can't go into details right now, but I will say a few random thoughts.  

Since you have two new 12 volt batteries I would stick with them until they die.

Places like Costco often have killer deals on the golf cart batteries (6 volts).

Two 12 volts in parallel = 12 volts, two 6 volts in series = 12 volts, so no change is needed on the charger/converter.

There is a special way you want to make sure dual batteries are wired when in parallel.  Make sure the + is tapped on one battery, and the - on the other battery.  It will ensure even discharges and charges.

What counts is watts, which is directly related to the amount of lead in a battery, so two batteries of the same size whether they are 6 or 12 volts will usually have the same total energy.  Where a 12 volt batt is rated around 110 amps, a 6 volt batt of the same size will be rated for 220.  Multiply volts time amps and you get 1320 watts either way.  So no real advantage changing to two 6 volt batteries since you already have the two 12's.  Where you may loose out is dealers usually get the cheapest batteries they can get and they are usually NOT true deep cycle batteries.  Often they are marine deep cycle batteries which are hybrids between deep cycle and starting batteries.  I've even seen dealers put starting batteries on the tongue.  The 6 volt golf cart batteries ARE true deep cycle batteries which will last longer.  So learn how to conserve with the batts you have now and then convert later after they die.  Remember that you should never draw the battery down below 50% state-of-charge (at least most of the time) for best battery life.  You can do it down to 30% once in a while but do it rarely.  See Wind Sun's battery faq for details.