should the below grade portion of the building wall be included in the wall area for purposes of calculating window to wall ratio in BeOpt?

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The wall area, for purposes of window-to-wall ratios, does not include the below-grade wall area. You can confirm this by drawing a building with a slab foundation type, looking at the absolute "Total Window Area [sqft]" that BEopt calculates for a given Window Areas option, and then changing the foundation type to a conditioned basement. Note that the absolute window area is unchanged.

That said, if you have a specific window area you're trying to achieve, you can create a Window Areas option where you specify absolute areas instead of window-to-wall ratios. See the "50sqft, all facades" option as an example of an option with absolute window areas that are unaffected by the drawn building geometry.