[dsraven]

a couple of tips you can try,
when welding 2 panels together that overlap each other, spray some weld through primer on the parts that will contact each other, then do the weld. that way there is no uncoated steel there to rust. it is near impossible to get a coating on these surfaces otherwise.
if mig welding always cut the wire tip to length prior to starting each weld so the wire is sharp on the end and will strike an arc right away, less spatter and better weld
always clean both sides of the weld area down to good clean metal so your weld will be good as well
for overlapping parts, drill a series of about a 1/4' diameter holes through one of the parts to be welded,spaced apart like the spots welds you had to remove, then put the parts together and vice grip or sheet metal screw the pieces together so they are how you want them (teck screws work well because they have their own drill bit on the end). then weld through the hole you drilled into the part that is behind so the two parts weld together well and you can see the puddle connecting the 2 parts. if you predrilled the right piece then that part will either be unseen where the weld is or else the weld area will be easily seen and cleaned up after welding to be smooth. a small hole can look like the parts connect as you welded but then the weld caps the hole so quickly you are really guessing as to whether the parts are actually welded or if the hole is just filled. practice on some scrap if not too sure.