Think I'd be for getting all the uglies cut out of the corners and getting some good solid metal in there before I started skinning the top....

Will you be using a ribbed or flat roof skin??? What are you planning on using for bracing from side to side to support the skin???

I usually get all the edges and the existing portion of the roof all straightened out, stripped, and prepped (no filler yet) , install the roof supports, then lay out a skin with poster board sheets cut to fit and taped together.... This will give you the opportunity to get a visual on the roof contours and basic shape before you start fitting the metal....
Much easier to cut and fit a piece of posterboard then sheetmetal!!~!!