Stitch weld it as is. if you want the extra welding, weld it from above as well. Keep your welder focused on the frame rail so that the majority of the heat stays away from the floor pans and you dont end up punching holes through them. weld nice smooth U shapes building up a puddle at the top of the U (on the frame rail) and then dropping down to the frame rail and back up. this will also help prevent distortion. And when i did mine, i welded the frame rails together to make one solid piece prior to welding to the floor pans to ensure the joints were not weak. Once you are done seam seal it and call it a day.