I am no body man and I can even tell you ....you dont fill in holes with bondo. If its accessible from behind weld in a plate from behind. If its inaccessible, cut out the bad metal, make a piece out of cardboard and make it fit. Then take the cardboard onto some sheetmetal and cut it as that template. Get some magnets, at least 3, make sure they can hold some weight, tack weld the piece on, grind down the welds. If you are unsure at this point and you arent making a decent restoration, dimple the metal around the seam you just welded and lay down some fiberglass. I dont care for bondo. If you care about the overall straightness of the car with this new piece, start block sanding but it sounds like you are in a rush and trying to keep water out of something....course...thats how I would go about fixing it but I dunno where you are working or on what