I've done both, first one I did I used fiberglass and some glazing putty to finish it off - it turned out good and painted well. The last one I welded a piece of sheet metal over the factory panel and it looked, well factory. Not that the glass didn't but the metal I seemed almost flawless after paint and I know that years down the road the metal will look better. I made sure to run the hose over the back end to make sure I had no water resevoirs as bad as these cars rust.
Matt
Matt