I paint my pieces with Zero Rust and let them cure prior to welding them in place. Also, prior to closing off an area, such as an inner cowl, I hit it again with more ZR. After I am done welding the new piece in place and grinding I spray the worked areas with ZR. After letting it cure I them seam seal the patch. In my opinion that is about all you can do without spraying everything with undercoating or bed liner material.