Hi Roy, it may depend on the type of calculation you are doing as to the best solution. The simplest option is to create an Exposed Wall in Fabric Data using the layer data for the above ground wall. Once created you can adjust the calculated U-Value…
The workflow for correcting a finished floor level can be found in our Support Solutions here:
http://communities.bentley.com/products/building/performance/w/building_performance__wiki/11959.changing-floor-heights