To run a program using command-line arguments, set up a new tool menu just like the one in step 3, but make sure you check off the box labeled "Prompt for Arguments". This will cause a dialog box to appear where you can type your command-line arguments (in the exact same format you would type them at the Dos prompt).
You could also check off this box in the tool menu item you created in step 3, and when you run a program that does not require arguments, click the "Skip" button in the arguments dialog.