Not much you can do. I typically paint the backside (side hidden once both pieces are welded together) with high temp paint. The welding process will still burn off the high temp paint immediately around the welds. If possible, the seams get seam sealer to keep out moisture.
If the repair is simply a patch, I avoid lap welding and use the butt weld method. But, I believe you are talking about two pieces lapped together and spot welded.
