I used a frame cap on my drivers side forward sub frame. I drilled 1/4" holes in it so as to put plug welds to adjacent factory subframe. I felt that only doing a seam weld at the top would not have the cap "see" all of the load that the factory frame experiences. Not to discount the seam weld at the edge though. I did as much along the edge as I could. I didn't go crazy and swiss cheese my cap though. I put plug welds in about every 3 inches and sort of zig zagged altrnating high and low on the subframe. I also put a few on the bottom where I could. I had to cut out about 11" in length X ~1" vertical out of the factory frame. I have pictures but they are too big to post here. Send email address to me if you want pics.
Before drilling out the holes, I called Auto Rust guys and ran my idea by them. They liked it but cautioned me to make sure the holes are big enough so that I could start the weld in the center of the hole and finish in the edge. They felt if the holes were too small, that I might cover over the top without adequate filling of the cavity. After the plug weld is finished, grind it off flush. You can hardly tell its there. I had told Tom about the brushable weld through primer. Its cheaper than the spray on stuff but same chemical.
Here is a trick that I learned. After putting your holes through your cap, slide it back onto the frame to be reinforced and clamp as though welding. Using a marker, scribe the holes onto the factory frame to be welded to. Take the cap back off. Cut pieces of masking tape in little 1/4"x1/4" (or what ever size covers) squares and put over the scribed circles. Paint the outside of the factory frame with the weld through primer. Paint the inside of the cap. Now, carefully remove the masking tape squares. Put cap back on, clamp and weld. I have read numerous places were people paint the whole thing and then get pist off about not getting a weld to start on the painted surface. Then they go back and grind off the places where they need to weld and everything works fine.
In a moparmuscle article where they installed a quarter panel, they ran into this problem. I guess I just saw this issue coming as welding just doesn't work unless the surface is bare and clean.