How you wire the PV modules will depend on the type of charge controller that you are using. Just because the charge controller manual says that it can handle up to 44.2V doesn't mean that it is able to step that voltage down to the 14-15 volts that a 12V battery bank would want to see for proper charging.
It is likely that the charge controller is capable of charging a 24V battery bank with a 24V nominal PV array. That would explain the maximum input voltage of 44.2V.
There are more sophisticated charge controllers that are capable of stepping down a higher PV array voltage to a lower battery bank voltage. This type of controller is called an MPPT controller, and while they are more expensive than other types, they actually do provide a gain in charging current over their less-sophisticated counterparts.
If you had this type of charge controller, then you could potentially wire up the 2 Kyocera KD135SX-UPU modules in series. This would help with voltage drop along the wire run, as you mentioned. I would only consider this method if you were CERTAIN that the charge controller is an MPPT controller, and the PV array input did not exceed the maximum power input of the controller.
To echo the other comment from Tom, what charge controller do you have?
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