I would think run the long panel in front to have one piece from the wheel well to the door opening.
I suspect that the old metal is not that thin unless your panels do not go far enough to get away from the rusted/thinned metal. Welding is going to be a better approach in my opinion. I know lap joints are not desireable but if you offset the new panels at the top to slide behind the cut off old you have double the metal thickness at the overlap/joint. It would be best if you can access the back side to apply seam sealer over the lap to prevent moisture from invading the joint.
