If you want to go the flanging route, punch holes in the main body and flange the patch and then hold together with sharp sheet metal screws insead of rivits. Then weld in the holes and then weld around the edges of the patch and grind down. Make sure you treat the patch panel with some weld through primer. You need to do something with the flange portion as it can collect moisture and promote rust down the road so seal both sides.Best way is to butt weld the patch into the original panel then you don't have to overlaped metal to worry about on the back of the panel. Eastwood sells some nice clamps that will actually clamp together two pieces of metal and leave the right gap to be welded up. If you use the same thickness of metal you can create a patch that once painted woudl be almost impossible to find.
In either case I use either fiberglass or all metal filler for the first coat over the patch since it prevents moisture from penatrating into the repair.
Go to the Eastwood site and look at their forum area there is some real nice information on rust repair another area to poke around in is Bautobodystore Forums good place to get answers