First thing with weld thru primer, don't apply it too thick. Second thing and this is a BIG thing, LET IT DRY THOROUGHLY that is the key big time. If it's not dry it's full of solvent which burns, and you can't weld through it worth a crap.
Another trick is to clean the weld thru primer out of the hole where you are plug welding, there is no need to have it there, you are going to me melting that metal together right, it doesn't need to be there. It's there to protect the surrounding areas. And if you are butt welding you don't need it anywhere near the weld, ti's not going to do jack for you. Protect it after you weld it with cavity wax or of course if you can sand and prime and paint the back side you do that.
Brian