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I've got some rust-through holes (under 0.25") in some of my sheet metal. My flux-core MIG has only two power settings and even at the lower setting I'm having trouble with the holes getting bigger through melting.
Get ahold of some copper plate and place it behind/below the hole you are welding up. The copper has a higher melting temperature than steel so you can literally weld right across the copper to fill the hole and then pull the copper away when you are done. It may stick slightly but it will not be bonded or melted in etc. A flat plate works well for flat panels, but some thinner pieces will be needed if you need to bend it to conform to a curved body panel.
I have used copper tubing, split and flattened out then cut into 1" squares. I held them in place with 1 1/2" dia. magnets available at Radio Shack. This allowed me to weld the holes up, without relying on someone else to hold the copper on the backside.
If you can lay your work flat (horizontal) you can 'puddle' the weld in the hole and cover a much larger area.
If I were you, I would think about welding in a new piece of steel. If the problem has gotten that bad then your metal right next to the area you are fixing could rust through next. Then you'll be perpetually welding in rust holes. By using a small cutoff blade you can cut out a square hole about 2"x2". Then make yourself a patch out of similar gauge sheet metal. The patch needs to just fit the hole. By tach welding one spot at a time alternating from side to side, then the weld will eventually by donwe and the metal won't distort. Good luck John