I cut the old quarters 1 inch below the top lip.
Then I cut the repro quarters so they are 1/2 inch below the top lip. (1/2 inch overlap) Tack weld about 12 inches apart across the panel and let cool. Then continue filling in between each weld, letting cool after each pass. Do this till you get a weld every 1 inch. Being close to the lip helps prevent warping cause the lip is the stiffest part. Also letting it cool between passes prevents excessive heat build up and panel swelling.
Then grind the welds slightly lower than flush with 60 grit on grinder and finish with body filler. You will only have a 2-3 inch wide line of filler and cant be seen inside. You can also finish the inside incase someone lays in the trunk and looks up.
When you wrap around the door post, remove the old wrap first or your panel will sit 1 metal thickness too high. Drill 1/4 inch holes in the wrap about 3 inches apart and weld thru those holes to simulate the factory spot welds. Or you can leave the old wrap and trim the repro quarter 1/2 inch from the wrap and do like the top of the quarter. Wrapping around is easier and less chance of warpage.
Also, have your doors on and the rear valance in place and make sure all the body lines are even before you weld. You cant correct them later. Make sure the door aligns with the rocker panel also. Then weld.
Good luck. Have fun.
