Insulation should be installed to fill the entire cavity. REScheck™ uses nominal insulation R-values. The assemblies listed in REScheck already have a default value added for standard sheathing (depending on the assembly component).
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Additional resources are also available from the Building America Solution Center.
The Building Energy Codes Program compliance tools -- COMcheck™, COMcheck-Web™, REScheck™, and REScheck-Web™ -- have the capability to upload and download files to and from the desktop and Web-based versions of the software you are using.