Air Punch Flange Tool

When I did my quarter I flanged the upper sheetmetal just below the body line and held it in place with sheetmetal screws - did not punch holes. After welding the seam I plug welded the holes shut. I used brushable seam sealer on the back - easy to work with. You should be able to order online or pick it up at your local auto body supplier. You can use the 3m stuff in a caulk gun. Most of the two part sealers require a special/expensive dispensing gun.

As an alternative to butt welding or flanging, I know some body guys will use a backing strip: http://www.autobodystore.com/door_rust.shtml