If you are running it under the service, you have to go into your contol panel, into the administrative tools, services and stop the service first.

If you are running it just in a cmd window that you either minimize or hide using TrayIt or one of the similar tools, you just press ctrl-c to close out the current run.

Once that's done, you go into your command line (dos) and go to the folder where the console is living and execute it with the -flag you want.

Note: This will only work if you are using the non-graphical (Not the Screen saver) version.

Hope this helps.