Regardless of the weld type/method, the metal heats up at the welds (and surrounding area) and realigns during the cooling process tighter than before, thus shrinking. This shows up as deformity and/or puckers as the weld and Heat Affected Zone (HAZ) shrinks while the remaining unaffected panel attempts to maintain it's original shape. Normally this is fixed by planishing the weld and HAZ by using a hammer and dolly. So when I'm looking at where to cut a panel for fitment, there is less of a concern about keeping it as small as possible, and more to accomodate access from both sides for planishing welds. The next thing to consider is availability to weld through a high crown or low crown area. For example, on the door skins, welding about a foot above the door bottom (low crown) you'll see when the shrinking occurs that the low crown is quick to flatten out, and more difficult to try and maintain the correct shape. Welding higher up just below the window, the panel has a higher crown, and while it still shrinks there, having more crown in the panel helps to keep the shape moreso than having the joint farther down at the bottom. It will still require planishing, but with the panel holding the shape better, it is easier to see where to address the issues.
Even though you're only doing floor pans (this time...), it is still a good practice piece to use this as a learning tool for the proper methods to use in other areas, as if it were a patch on the outer part of the truck, a door skin, for instance. Then, you'd be less apprehensive to tackle those areas that will be seen, and more likely to be successful doing so.
Where some may say that flanging the panel and welding in is easier, you will have to deal with the dirt and moisture trap of two layers (I call them rust generators) and trying to planish those are near impossible. Any time you have one thickness to one side of the weld, and two thicknesses to the other, the weld will not planish effectively and if this is an exterior panel, you will also see a ghost line in the finished and painted panel as the thicker side will have a different expansion rate than the single thickness metal.
Here's a thread that does have quite a bit of info for welding in patch panels.
http://www.garagejournal.com/forum/showthread.php?t=53534 
