Fenestration is considered anything that transmits light, however, COMcheck cannot calculate fenestration without having a wall associated with it. In this case the wall is entirely fenestration therefore, the square footage would be the same for both the wall and window area and the software will calculate the wall area as net zero since the fenestration is the entire wall.
For the spandrel glass or translucent wall systems the way to enter that into COMcheck would be to first define a wall by choosing wall as "other" from the drop down list of wall assembly types, enter the square footage of the wall system (e.g. 100 sq. ft), enter the U-factor for the wall system (e.g. 0.23) and also you will need to enter the heat capacity of the wall. For information on heat capacity and how to calculate it, in COMcheck, go to the help menu, help topics and wall software inputs.
After defining the wall, define the window area by choosing window as "other" from the drop down list of window assembly types, enter the square footage of the wall system (e.g. 100 sq. ft.) and choose option two under Fenestration details "Product performance tested in accordance with NFRC", if you do not have a product ID, enter "NA", then enter your U-factor and SHGC values from the product manufacture specifications.