LEED/PRM Modeling

[kbeason]

I am modeling a LEED submittal. The building underwent renovation/alteration. Floorplan areas were not changed. The building layout isn't really complicated in that it is 2 square floor plans (one 2 stories, one 3 stories) connected by a conditioned walkway in the second level, or first floor for the EU readers. I am using the PRM Navigator and am unsure how to implement Appendix A of 90.1 in context of baseline constructions. For example, I know the material constructions of the building before the alteration work was completed, but would the constructions of the baseline need to be adjusted such that the U-factors reported by VE match those listed in Appendix A?

Also, the window in the baseline are essentially like storefront windows on one of the square floor plans: 100%. In the proposed/alterations, the window areas are less than that by virtue of adding a sill wall of 3' height around the perimeter. Should the baseline building reflect the max 40% area as referenced in G3.1(f) Baseline?