Are you boxing the frame? Welding closeout plates into the "C" channel? If you are then go ahead and do your stitch welding. Then weld some more after the welds cool. Keep stitch welding and cooling until you have all of the plate fully welded. Insetting the boxing plate a 1/4" or so is OK.
JB Weld will do nothing to add strength. Waste of time. Just keep doing as you are doing until it's all welded.
Mark