What I do for these is take my matching sheet metal and use my spot weld popper. It's like a hole punch for doing spot welds. I then save the little circle that comes out and use a magnet to hold it in place. Tack it, Grind, tack etc. Then hammer and dolly as needed.
Every time you take metal up past the plastic point it shrinks.
You correct shinks with hammer on dolly work to stretch the metal the has shrunk.
Mig welding can be tough. You really need to get settings right to lay a thin bead. To correct for shrinkage you need to grind smooth and hammer on dolly. Copper shaped to the surface can help reduce work, but does little correct for shrinkage.
Small holes can be filled using a MIG and getting TIG rods of the same material as the wire. You back the hole with copper. Lay the TIG rod into the hole (touching) and start the arc on the tig rod and feeding in the tig rod to control heat from the arc. This prevents the burn back you can get at the edge of metal from too much heat.
You will want some small wheels to get the metal sort of level before you correct for shrink. You might also be better off welding on the inside as you will need to do more grinding on the side you are welding.
Larger holes or even smaller holes it would be good to have some premade rounds. I think there is a low cost tool you can get at harbor freight. Look up on youtube for making a ring out of a coin. They show this low cost punch you can get that may be a good thing for you.