Schooner,
  What model of welding unit are you working with? it sounds to me like you may be using a smaller wire feed welder that has only 2 settings. Voltage (Heat) and Wire Speed (controls the speed IPM and Amperage). these are (tapped settings), which means there isn't much in the way of fine tune for either of the settings. Look at your machines owner/operator manual, and determine what values are given for each of the tapped settings. Also what Gas mixture are you using for Your shielding gas? IMO, for the best results on light gauge sheet metal, I would run my unit at approx 17 to 20 volts with a wire feed speed of approx 180 to 225 IPM. these setting I refer to are for runnig beads on light gauge sheet. Running stringers (beads) on really thin metal will cause heat distortion in your metal. I would also use a higher Argon to co2, or Argon to o2 mixture. The Higher Argon % helps to cool and freeze the weld.
As for spot welding. IMO, I would spot/tack weld all the way around using a back step pattern until the patch you are making is complete. Space your spot welds with approx 2" distance between them after you have tacked the patch into place on all four sides (or in the proper places if the patch configuration is not sqaure or rectangular)  and don't be in a rush to get all the way around, as this too will cause heat distortion.
As for your problem with burn through. That may be caused by improper gun angle, too much heat or trying to run beads on your metal. If I am correct about the type of welding machine you are using, it probably has a setting for running (NO-GAS) wire. If this is what you are using...Stop. That is Flux-Cored wire. It is not suited to the type of welding you are attempting.
  For the hole you have burned in your metal, Use a non-ferrous metal backing strip i.e. brass to re-enfource the back of the holes and fill the holes using the proper wire, heat and shielding gas.
You can obtain a manual for auto body repair at your local auto parts store. "Haynes" has some pretty good manuals.
I am sure you will get some very experienced weldors to chime in on this with far better advice than i can give. Remember, this is only based on my opinion which is worth about 2 cents.
Respectfully, Jeffrey Grady