Manual vs. Automatic Navigation
There is an option to create a manual menu to be used in the site’s primary navigation. However, the preference is that all sites use the automatically generated menu. Regardless of your choice, the website should still use a proper site hierarchy with very few pages at the top level.
The advantage of the automatically generated menu is that all pages within a site will be available in the navigation without the editor having to remember to add it. If there are pages that you do not want to be made available in the primary navigation, there are settings at the page level that can accomplish this. The order of the automatically-generated menu is alphabetical by default, but this can be altered by setting different Order values for each page.
Manual menus will come in handy on the root site, due to the ability to link to subsites within that WordPress install. However, the manual menu structure should still represent the hierarchy of the site.