You will need to know the wire length, panel voltage, and refer to a voltage drop chart/calculator to know if the existing wires are sufficient.
Assuming wire length of 20 feet and 5 amps at 18 volts coming out of the panel. 14 AWG results in almost a 3% voltage drop which is typically considered the the maximum drop. Lots of assumptions there so run the real numbers to be sure using a calculator such as (there are many): http://windsun.com/Hardware/Voltage_Calc.htm
I do not believe any controller can properly charge two independent batteries from one pos/neg cable. The controller needs to sense battery voltage to know "how" to charge the battery - if there are two batteries connected (not a bank), the controller will not be getting accurate information. Are you sure you do not have two 12V batteries wired together in parallel to create one 12V battery bank? (a charge controller CAN charge a bank of batteries).