The main navigation of a site does not change often. In fact, many sites never have the need for main navigation links to change. Main Navigation links are commonly a representation of folders at the root of the site. Sub navigation links (level 2 links) are commonly the folders within the main folders. This navigation technique allows for logical placement on content within the site.

This approach does not always work.

Omiting folders from navigation
There are many needs for folders to exist at the root of the site which should not be considered main navigation items. It is easy to omit folders from showing as menu items. Select the 'Advanced' tab in Edit Mode and click on the Omit this folder from Navigation and click Save. This will remove this folder and its subfolders from rendering.