I agree with Wagesofsin. I did it both ways with two different cars and had the same situation with a lap seam on two different floor pan and trunk pan locations. I would check however if the wheelwell to quarter panel is good and rust free as it would be better to change the whole quarter panel than to pay for it later.
Instead of the saw I used a Fein tool with a very narrow sheetmetal blade to cut the two panels at one time. This left a very small gap and aided in eliminating most of the blow out at the seam when I welded it back together. Remember to start your wand away from the seam and draw it across the seam. I learned that the hard way and had the holes to prove it.
