If you simply run the WebConfiguration application it runs in 'visual' mode that shows a Windows Forms UI. You can also run the application in non-interactive mode by adding a command line switch.

WebConfiguration -u

runs the application in unattended mode. When running in this mode, the application reads the XML configuration that has the same name as the running application in the current directory and simply performs all the tasks that are filled in.

Note that the path the application runs in is important. You should make sure that if you run a batch file of some sort that you are running in the directory where the EXE exists, because the XML file contains path information in relative paths. If the EXE runs in a different path these paths will not be valid causing invalid settings to be made possibly.