The text you put in the Command line box is broken into 'words' and passed to your application, which can access them using argc and argv in the usual way. argv[0] is set to the full path for the application you have selected.
Debug application
Tick this box if you want to use Code Composer to debug your application. With this option selected, the server pauses after loading the application to allow you to pass control to Code Composer. This is described under Debugging.
Report application termination
Tick this box if you want the server to bring up a notification when your application stops. This box is ticked when the server is first installed.
Tick this box if you want the server to clear the output display each time you run an application.
Standalone application
Sometimes you may want the server to load an application but not attempt to communicate with it afterwards. Ticking this box stops the server from attempting to communicate with an application once it has been loaded. Selecting this option makes the previous three options meaningless and will disable them.
Run application when selected
Tick this box if you want an application to be run as soon as you have selected it using File or . Clearing this option means you have to start the application explicitly using 
or Go/Run. This box is ticked when the server is first installed on a PC.
Run .app files
When you launch the server by double-clicking a .app file or by giving a DOS command, the server normally attempts to load and run the given application, providing that there is only one hardware interface installed and that only one DSP board is found. If you clear this box, the server simply selects the application but does not run it.
C4x application
This option is no longer supported and only remains for the benefit of long-standing customers.