To run a COBOL program you simply enter the program's name (if the program has been linked to a system executable program) or use the run command (if it has not). Both of these actions behave in Visual COBOL Build Tools for Windows in exactly the same way as they do in Visual COBOL.
See Running an Application from the Command Line for full information on both of these methods of running a COBOL program in Visual COBOL Build Tools for Windows.