In a nutshell the process was:
Jack up car, remove rear wheel and wheel well liner, remove rear door, remove door weather stripping out of the way, cut away rocker panel near the rust and determine how much you'll need to cut away to get to good metal. Strip away paint, cut replacement panel down to size needed (they're sold from front to rear wheel arch), cut existing panel so it's a bit smaller of a hole than needed. Test fit new panel and mark where cuts will be, carefully cut away existing panel (don't make to big of a cut), test fit again and grind away existing / replacement panel where needed to ensure good fit (this took a lot of time). Apply weld through primer to bare metal that you won't be able to paint later. Patch body where needed (don't worry my weld was much better on the other side). Weld on replacement panel, grind welds smooth, apply bondo (I used the fiberglass kind because I think its better with water), paint (I used 2k primer, paint and clear spray cans), spray cavity wax (I used 3M cavity wax, a whole can, and their applicator wand) in the space between the rocker and body, apply seem sealer. I sealed up where that wheel arch thing screwed...reinstall wheel / liner, door, etc.