There's lots of different methods, and two that I employ are either using buttwelding clamps to hold the metal in place or tacking a stud to the patch. With the welding clamps you have to have access from behind to assemble them to the panel. Most of the time I just use my stud welder and weld a stud to patch either in the middle if it's a smaller patch, or for larger patches, wherever you need to have the stud to hold it. Then you can hold on to the stud to get it in place.
I make sure the entire patch fits nicely in the opening first. Then I put it in and tack one corner in. This corner will be however flush you want it. Then you tack in the rest of your corners and finally the rest of the weld. Because you have the studs attached, you can pull a corner out if it needs to come out before you tack it. It really isn't too difficult at all to get it as flush as you want it. Keep in mind you need some space for filler over your weld too so you don't have a bulge. You will need to jump your tacks around and let them cool naturally so you have minimal shrinkage distortion of the metal.
A lot of people do overlap or flange welds; I've never done one. All my repairs are made with buttwelds, and I think they would be much easier to do than an overlap weld.
If you don't have a stud welder you can tack some nails to the panel. You just cut the nail or stud off when done and grind it down there if need be. You may have to put some glaze over that area.
