Adding to what bigchief said. I recently replaced my trunk floor and would highly recommend butt welding the trunk in. it depends on your skill level and value of the car but my opinion is that this is the best way to repair the trunk and not worry about over lapping metal that can collect moisture once sealed up and start rusting again.
Most professionals who start replacing inner and outer wheel wells and as much as it sounds like you will do, will have a jig for the car to be positioned on to insure nothing moves in the process of weakening and cutting the old stuff out.
If you don't have a jig to position the car, I would definitely weld braces in to keep your alignment and even though you won't replace the quarters, they can/will move if you don't brace properly. Just my two cents. Good luck with the project.
