The Schedule R form can also be adjusted.  If you place any numbers in Lines 5a, 5b, 5c, or 5d, then the form will calculate the entire 941 Form.  If you are only populating Lines 5e on the Schedule R as is shown below, then you will have to manually add the values for Lines 5a, 5b, 5c and 5d on the 941 form.   The main EIN will always be present on the first line in the software, but will print in the appropriate place on the printed version.