There is another method. It is called a "toupee".
You chop it in 1/4s, then after the four quarters are reattached... and you have filled the gaps about 6" above the windows... you cut the entire center out of the roof, right where it starts to flatten out on top.
At that point you use the top roof panel from a donor truck, or something with a very similar shape... cut it to match the dimensions of the hole, then weld that in.
The point of all of this is the have your bodywork around the edges only... and not have to struggle,trying to get the patched up area on top straight and smooth again.