I have been fixing up a few pinch joints on my vehicle the past few months that sound similar to what you want to do.
NOTE: Please understand that I am a complete novice in bodywork. THis is my first restoration and I am learning as I go. Here is the method that works for me:
I first drill out the spot welds using a spot weld cutter in order to seperate the pinch joint. Then I strip any paint or debris to get a good look at what is rotted. Next, I grind away any excessive rust to get an even better idea of how much corrosion is really there. I mark the area that needs to be replaced. I do NOT cut anything out yet. I begin with a flat piece of sheet metal. I cut it to a basic shape of the rotted area plus an inch or so over on all sides including about an inch overhang over the edge of the pinch joint. Then I start to form it to the curvature of the panel/pinch area. I found that just laying the new patch panel over the existing area and carefully working it with a pair of vise grip clamps quickly conforms it to the exact shape of the existing panel (I wouldn't suggest this for large patch panels but it works great on small shapes). Keep in mind, that if I was to cut out the existing rotted out section I wouldn't be able to shape this patch panel as easily.
When I finally have my patch panel conformed to the body curvature. I then place it over the panel and trace a line around it with a Sharpie marker. Then I remove the patch piece and cut on the inside of my line. Finally I install the patch piece and do any final fitup by filing down the patch piece to get it to fit nice and tight. I still let my patch piece extend past the inch past the pinch joint, this helps with welding. I find that it helps prevent blowthrough when you do that tack right at the edge of the pinch joint. I spot weld the patch panel in and then weld it up between each spot weld, carefully letting each weld cool down before I continue on. Then I grind the weld down smooth being carefull to only grind the weld bead and not the new steel around the bead. After I have the piece welded in and ground smooth, I cut or grind the overhang off such that it matches the pinch joint.
I've had a couple situations in which I had to replace multiple layers of the pinch joint. I use the procedure above to make the top layer of the pinch joint except I stop at the point of welding. Then I start over again with the next layer, then the next, etc, etc. Once I have all layers fabbed up, I weld them up from the innermost on out. you just need to make sure that your top patch piece is larger than any rot in the innermost layers of the pinch joint.
I have learned the hard way to never completely cut out the rotted area until you have your patch panels already formed, trimmed, and test fitted.