All pin holes should be welded up. Any filler that you put in will eventually fail and rust will form. I agree with jomichael and use a light behind the panel too see any pin holes and weld them up. And as MPandC said the "dot" welding method with over lap is good. I might add that if you grind each dot after welding it , it will be easier to see where you are and weld the overlap at that point. Another advantage of this technique is that there will be less chance of warping the metal if trying to grind the entire welded area at once.
