You have great panels, at about the right open circuit voltage (VOC). If you run them in parallel, your wiring into the controller is at 18 volts at best. In that scenario, I doubt you'll see any difference in PWM vs MPPT charge controllers. So use a PWM controller which is more robust, and costs less. At 36 volts(ie in series), the same amount of power can be sent to your battery at 1/2 the amperage, resulting in less voltage loss, and less power lost to resistance heating. In the latter case you need an MPPT controller to do the DC to DC conversion and operate at max efficiency. Running a 36 volt panel into a 12 volt PWM would waste half of your solar power (wattage).
What gets lost in these discussions, is that these are very low power systems. Under 200 watts (or even 400 watts) the difference between PWM and MPPT is very small measured by a power meter into the battery. MPPT will always be better theoretically, but if you are running standard "12 volt" panels (VOC 18 or so) the difference is minimal. It's when you get into higher VOC panels that MPPT controllers really shine, because they can do the DC to DC conversion need to take advantage of the higher voltage panels.
I think your situation is an ideal one. You can run with an MPPT controller to take advantage of the inherent capacity of higher voltage panels/wiring(ie in series), or if something fails, you can use a cheap PWM controller and still get most of the function with some changes in the wiring(ie in parallel).