Use both by putting each's controller on the same battery bank to add their amps. You can have the roof one with installed wires and the portable controller output to wires with clamps.
You want the controllers to be near the same "high set point" voltage, but the roof panel and controller can be different brand/model/size from the portable's.
Only thing that needs to be nearly the same is their output voltages so they add their amps. (and be for the same battery voltage ("12v", "24v", whatever) You can even have one set MPPT and the other PWM, doesn't matter.