A present you have two 12 v batteries wired in parallel to the converter/charger. Like this, except in place of the trickle charger is your converter/charger.
To change to either two or four 6v batteries, wire them in series, in pairs, to the converter charger.
Photograph the present set up and label all wires before removing the batteries and connections. I'm sure there are additional wires to hook up items not controlled by a battery isolating switch or relay. Be sure to replace those connections to the proper polarity, if in doubt have someone knowledgeable in 12v wiring to help.