The Menu Builder settings section offers a variety of ways to create navigation menus in Builder. The "Pages" and "Categories" sets of checkboxes are the original Menu Builder offered by Builder. Using these is not recommended.
As long as your site is running WordPress 3.0 or above, you can use the powerful Custom Menus editor built into WordPress and found under Appearance > Menus. It is highly recommended that you use WordPress' built-in custom Menus editor.