Michael,
Sure, the process is not very hard just follow these steps:
1. Open the FlexViewers Project properties (right click FlexViewer in the package explorer window and choose properties).
2. Switch to the Rub/Debug Settings page
3. Select the launch configuration in the window (mine is index (2)) and click the edit button
4. Down in the url or path to launch uncheck Use default and add your config parameter there.
5. Apply/Ok that dialog and you are good to go.