Repairing rust and weak holes on a steal boat is a seemingly-constant process. Repairing weak spots or weak holes requires a bit more skill, as it will involve welding and possibly burning, depending on the thickness of the repair material. Both types of repairs will involve painting in one form or another.
Chip off deep rust. Use a chipping hammer or hand-held grinder (with a steel brush attachment), followed by a wire brush. For deep pits, use a needle gun; fill and level resulting needle marks with Red Hand putty before applying rust converter or paint.
Leave a thin film of rust on the metal for the rust converter to adhere to. Apply a generous amount of rust converter, including the areas beyond the edge of the rust. The clear rust converter will turn black when it is completely dry.
Patch small holes above the waterline with Red Hand putty. Mix this two-part epoxy putty in small batches--only enough for the immediate job. Apply the putty with a paint scraper. Do not attempt to level the putty off, as it will shrink during the curing process. Wait until the putty has completely cured, then grind or brush the surface to level before priming and painting.
Cut sheet metal into patches that are at least 1 inch larger than the hole or weak spot.
Weld the metal patches in place to cover the holes. Inspect for "cold welds" by hitting the weld with a hammer. When the welds are cool to the touch, grind only as needed to achieve a smooth, secure weld.
Prepare the epoxy primer. Prime all new metal surfaces, all welds and all areas where the rust converter has turned black.
When the primer has dried completely, apply the epoxy paint.