As mentioned in the overview, the navigation has two levels: tier 1 and tier 2.
Tier 1 is page-independent. In the backend, tier 1 items align flush left.
Tier 2 is page-dependent. In the backend, tier 2 items are indented underneath their parent elements.
All you need to do to adjust the menu structure is drag and drop items where you would like them to appear.
Note: You should not nest items below tier 2. Doing so will mess up the navigation’s spacing.