I think you're confusing perhaps Copy File tasks and Run Script tasks.
A Run Script task would never have any command-line switches, because all it does is create a file and execute it. If it's a command script, we create a bat file and fire it off. VBS, we create a CScript and fire it off. Why in the world would we want a command-line switch to go with... a command-line? I don't get it. Just put it in the command script and.. you have your command line switches.
What am I missing? Perhaps you can tell us what you could do before that you can't do now so we can direct you accordingly.
Thanks!