I agree with 4dabird. Plus I just don't like disturbing good jams and seams that the factory made that are good. I'm going to do mine with just panels, my rust is similar in amount to yours (plus extra $$ for full quarters is out of my option).

I've seen the seam done 2 ways, one on the face of the quarter, and the other goes up and over the lip of the quarter. Honestly I've been thinking about going over the lip since that is the way the patch skins come I think and it gets the majority of the body work up and off the side of the car where it may be more noticeable. My friend did it this way and it looks almost perfect, just a little bondo shrinkage at the seam area of the drivers side quarter, nothing a few extra weeks or months in the sun could have probably taken care of. Either way the seam goes, I also read that a good way to line it up is put the quarter on mock fit (where most of the old quarter is cut off) just enough remaining so the new quarter overlaps a few inches. Then tack it in place. Then cut a line threw both panels (thin cutting wheel), that way it lines up perfectly where you want to butt weld the seam (I think that is the preffered method)... Make sure to goes slow and tack left side then right and back so on so on.. just my two cents, I really haven't done one before so be interesting to hear from the others that have !!