This page of the demo shows all the positions and their names:
http://www.shape5.com/demo/index.php?wp/fusion?page_id=204"Top" is the correct location to place a custom menu widget in order to mimic the "extra" menu on the demo.
The actual site menu cannot be replaced with a custom menu; that theme was released before the WP3 custom menus and uses the site page structure to determine the menu structure.
If you want true flexibility, I recommend looking at the newer/newest releases and seeing if there's anything on the Vertex Framework that can meet your needs.