So far I've heard of about three ways to go about trimming the replacement skin for a butt weld.
1) The cut through method that your looking into: The more we hash it out the less I like this way. No matter how you "slice" it there is going to be at the very least 1/8" of material missing (thickness of the cutoff wheel). And like you said, how do you keep the replacement panel fixed to the car as your cutting?
2)Trim the replacement panel first. Estimate how much of the panel you'll need, trim it,screw it or cleco it to the car and then trace outer edge of the panel onto the car. Then carefully cut on that line and you should have an exact replacement panel.
3)Trim the car first. Layout what you would like to remove out of the quarter panel, cut that off the car, and then screw the replacement skin to the outside of the car. You can then trace from the inside of the car, onto the inside of the replacement skin what you would like to remove.
I havent done it yet, ive just been researching like you. On my quarters I plan to butt weld and so far am leaning towards either #2 or #3. I think my car was hit from the rear and the very rear edge of the passenger quarter panel is wrinkled ( as well as about 6" of the upper quarter panel body line-or "hip" as I call it.) Right now my car has skins on it that are rotted out and the last guy just overlapped them. There's maybe 2" of original meat left from the body line down. I plan to cutt 1" down from the "hip" and have my seam there, until I get to the bad portion in the rear. Then i'll utilize the 1" lip the quarter skin has from there on back. So my seam will travel along the side of the car (1" down from the hip, and then jump up to the top of the car for the last foot or so).
I dont know if I communicated all that right, but I cant think of another way to say it.