What I usually see is everything dissassembled, repaired, epoxy primed, Test fit sheetmetal lining up all gaps etc, test fit anything else that goes on the car (trim, grill, mirrors, sill plates, door panels, everything cause you don't want to fix it after paint!), with sheetmetal still installed (but nothing else) block sand the car, block sand the car again, block sand the car again, wet sand the car, carefully remove the sheet metal keeping track of any shims and where they go, paint all the sheetmetal base & clear, paint the unibody base & clear, extremely carefully reinstall sheetmetal, color sand, buff, polish.

Note: This is different from the OE procedure which is basically to apply a rust preventative to the metal to metal contact areas (like under the door hinges), Then install all sheetmetal, and primer then paint the car. Any areas that get missed, Oh well.

Tav