If you dont already have an inverter or anything else that you are wanting to use that needs 12v then I would suggest using your 4 batteries in series for a 48v system. Looks like you charge controller is capable of it. Higher voltage requires less current to deliver the same amount of power, so you can use much smaller (and much less expensive) wire.
Wire your solar panels into 3 strips of 4 panels connected in series, putting the 3 strings in parallel. This way your wire will only need to be able to handle 15A max current instead of 60A if you ran a 12v system.
The downside is that if one panel in a string gets shaded it will effectively block power from the others in series with it whereas parallel panels wont be affected. You will want to strategically arrange your panels according to any shadows you might have. For example if there is a situation where shadow could cover 3 panels you want those to be 3 from the same series string so only that strip is affected, so you still have 2 strings making full power. Rather than 1 panel from each string getting covered which would completely tank your power output even though the 9 other panels are in full sun.
Good luck