In picture 1, that circled area would be spot welded by the factory. I would recommend that you use a spot welder bit and drill a couple of spots in the top, then weld them up, then cut the welds that you are there right now. That way nothing is moving plus you dont have to use any clamps.
As for picture #2, you shouldn't see those welds because that area should be seam sealed. You need to push seam sealer in there to keep water and crap from getting between those panels. This is done from the outside and doesnt take a lot. When done, it should look like 1 undisturbed seam. That said, you have to go out of your way to really see it when done.