Mouser - there is another way.
A normal commandline switch will run a new instance of the program, which would require your program to detect an already running version, do it's thing, and then exit.
However, if you add a hidden window with a textbox and a submit button to SC, then you can create a second commandline app that finds that hidden box and types commands into the text box and pushes the submit button. The second app will do nothing more than receive the commandline, post the simple text, push the button, then exit.
This way, you practically get commandlines to a running application without having to exit.
I have an autohotkey sample of this if you want.
I also made this post on StackExchange
about a different method using C#.