'50 chevy 3100

[dsraven]

that is how new vehicles are assembled as well but they also use adhesive in the seam along with the spot welds. with that said I would think if you spot welded, or basically drilled through the top layer like you said, every couple of inches, like the factory did, you should be fine. use seam sealer to keep the weather out on both sides of the seam. less welding=less possible warpage. small sections at a time with spot welds may make for a nice flat panel. if you are drilling holes anyway they could be used as screw holes or cleco holes to hold the panel in place while tacking. those holes would go right through both panels then of course.
when welding ensure to cut the wire each time for a nice chisel tip to strike the arc with. also ensure the steel is clean on both sides so no contamination gets in and causes porosity (bubbles in the weld), then paint and seam seal. a gas mig weld would definately make a nicer weld than the flux core. experiment some with how big you need to make the hole to weld through so you get the knack for attaching the weld puddle to both pieces. lots of those plug welds look great but only attach to the top piece of metal so there is no integrity. in that case it would be better if the part was simply rivetted using the proper rivet tecnique and composition of rivet of course, like aircraft.
see my example of how I used cleco's on the rear floor panel. like a spot weld done through each cleco hole. I did have to drill each cleco hole a bit bigger to get a decent weld through and be sure to check the back side to see if you have made penetration enough to sort of bubble the metal on the back side of the weld. otherwise you may just be filling the top side hole and thinking it is all good. sometimes the cleco "through hole" makes it easier to see that the weld puddle did attach to the bottom panel. practice makes a better "project" job for sure.
just my 2 cents.