Sorry to say it turns out I was mistaken and there are in fact two 6V batteries connected in series to make 12V.
It was possible to rearrange the batteries into parallel leaving me with 6V out.
Is it as simple as connecting the positive and negative of the battery to the two wires that would match to + and - on the Ardupilot ports? With the remaining signal wire being plugged into the Ardupilot as was before?