My opinion is to weld thru the thinner material. If you punch holes in the thicker stuff you run the risk of not getting the proper fill or penetration. I plan to punch holes in the floor for the front, rear, sides and floor brace areas.

You might fill the hole, but not have a good penetrated weld. I will avoid welding on my back at all cost. It's not as safe and gravity will want to take over. My .02 cents.