I have had good success with patching small holes with epoxy. Try to get as much of the rust sanded or removed as you can. Having something solid to bond to seems to work best. You may want to treat it with a rust retardant. Then I use a good epoxy and 2" wide masking tape to form a patch. I usually start with the lower side (bottom) if you can get to it. Put a small blob of epoxy on the tape and center the epoxy blob over the hole and apply the tape to the repair area. I try to leave the epoxy a little thicker where the hole is. The tape keeps the epoxy from running and keeps it in place till it dries. It may take several applications to fill all of a larger hole. Normally a 1/8" hole will be around a nickel to quarter size epoxy patch. The epoxy likes to run down hill till it sets up, (the reason for the tape). I have even patched holes on the bottom side of the metal, and the tape keeps the epoxy from dripping off till it sets up. Peel the tape off when it hardens. You can grind or sand to finish the surface. I haven't tried to patch a large hole, but I don't see why you couldn't glue in a piece of sheet metal to fill a larger hole.
This isn't real fancy but will work!