If it's not too deep and more of a line then I'd use the pen, the spray is better when you need to use some sandable primer and need to build-up the defective area. I recommend taking off the wheel and doing it away from the car so the metallic paint won't stick to the fenders.

As for your clear coat, I'd wet sand it with 2500 grit paper and then polish it and wax it to make it look like new.