Repairing small section of rust on the body

If you were closer I would come give you a hand. Do you have a replacement panel you are using or just making a patch? Either way grind off the paint where you want to replace the panel. Then trim out the rusted area's. Then get your panel to fit, and mark it on the car and trim along that line. Then you can weld either a lap joint or butt weld it. Recess the welds and grind, then do your filler work.