While MIG welding is likely the most prevalent used by the home hobbyist (as well as many businesses) it isn't the most user friendly in preventing damage to sheetmetal panels as you are experiencing. Some thoughts: (actually a lot of thoughts...)
Any welding operation is going to cause a certain amount of shrinking. Welding in a square-ish repair panel (for example) toward the bottom of a fender will induce a certain amount of shrinking and distortion, in four directions. By extending a patch to the wheel opening, and all the way to the bottom of the fender, you eliminate two weld seams, and half as much shrinking. If you can replace the complete lower fender from wheel opening to door opening, to the bottom, now you are down to one weld seam, and all the forces are pulling in a similar direction (as opposed to what you see with two intersecting welds) and the distortion should be less.
If you can trim your joints to zero gaps such that a no-filler weld (fusion weld) can be performed (Using TIG or O/A), then you should have about as small a HAZ as possible, and as consistent in width as possible, for less distortion. To explain this further, various starting and stopping in your weld will cause inconsistent width of the HAZ, along with the shrinking effects that come with it. This may lead to a "wavy" distortion. Consistent heat, consistent speed, without stopping, in performing a fusion weld will help to keep the HAZ, and all the other conditional reactions consistent, for less distortion. Having said all that, this example was for use with a TIG or O/A. Most enthusiasts will be using a MIG welder (as that's what they have) which is not very compatible with a full pass weld when dealing with sheetmetal. But you can still apply the same principles of consistency in using a MIG and "dot" welding. Single dots, skip around, use same overlap, same size dots (elapsed time of trigger pull) etc. This won't make the weld as nice as the fusion weld above, but it will help with consistency. And the biggest thing is to practice on some scrap pieces the same guage as you'll be working with to insure your welder is set up correctly for a full penetration weld. It's hard to be consistent if you're putting in the patches and still fiddling with welder settings, (practicing on the good stuff).
Where the TIG or O/A fusion welding does require some additional skill/dexterity over the "point and shoot" of the MIG, it by far is the best method to minimize damage to panels. Done correctly, typically the weld on the back side is nearly flat with little if any weld protruding form the back side. If there is weld proud to the back side, you will usually see a slight depression on the outside, that can easily be raised with minimal hammer and dolly work, flattening out both sides simultaneously. This in itself eliminates much of the grinding effort required to dress out welds like when using the MIG. Where the fusion weld may not be a viable option for you due to eqpt availability/skills, this hopefully will impress the importance of consistency in whichever method you use.
Short of having the ability to use the fusion welding method to minimze damage, I would recommend either using repair panels that will come up far enough to allow access from the back (ie: above the inner panel) for hammer and dolly work, or opening up the inner panel to allow this access. This would need to be done with some good planning to make closing it up later as painless a process as possible.
Here is a thread that shows using the fusion weld process. I hope to get to this point in the future, but still need to get past the teaching old dogs stage....
TIG fusion welding process
