The Navigation section remains the same across the entire demo site. For this reason, it exists in the default Widget Override menu. It is also a fairly simple section to set up.
The Gantry Menu widget should be set to match your site's main menu as it serves as the primary menu widget for the entire site. You can customize this menu by navigating to Administration -> Appearance -> Menus and creating or modifying your selected menu there.
Here is a breakdown of the widget options for this menu widget. Any options not present in this breakdown are left at default and should not be adjusted.