Hey Bobby.. So Im assuming you are laying the panels down with an over lap and gonna use some plug welds. Not a bad idea. If so you dont need a large hole at all. The thin sheet metal will be fine with a small plug. More smaller plugs is better than a few large plugs. Is it a MIG process? If so a 1/8" drilled hole is fine.
Use alot of heat. You want to be able to just zap it for one second. If your machine is powerful enough that should fill the entire 1/8" hole. Aim for the center of the hole, pull the trigger, keep the trigger on till the sheet metal melts into the puddle that is formed.
For plug welds and MIG I like to increase the heat setting way beyond what you would use for the sheet metal or the frame under it. And I lower the wire feed a lil. What this gives you is a solid melt of the frame and easily melts the edges of the sheet metal in by about a 1/32 to 1/16 inch. If you dont completely melt the frame then you just sit a cold nugget on top of the frame, with the sheet metal looking like its welded. And with a high current (heat) and slow wire feed the frame gets molten and the sheet metal gets melted and the nugget is pretty flat. Not much higher than the sheet metal. A solid weld.
The key to plug welds is to be able to get the bottom metal molten before the hole is filled up. HIGH HEAT, almost max for the machine. Kinda my pet peeve with welders, not enough heat. Yer melting metal. Crank it up. I know when Im hot enough when Im blowing though 1/4" plate. Its set right, I just need to move a lil faster. I like to weld HOT!!! Even with sheet metal, hot is fast, fast is less heat soak over time. And Ill cool in between my passes if its body panels. JR