The Navigation option under Design > DESIGN (on the left menu of the Back Office) is mainly intended to help you customize your online store's navigation experience. The default navigation of your store is based on the categories defined for it under Products > PRODUCTS > Categories.
You can use the Template Editor to call up the variables for in-store navigation. You can then modify those variables under Design > DESIGN > Navigation (on the left menu of the Back Office).
NOTE: The Navigation option is used mainly by Lightspeed's partners and requires in-depth knowledge of HTML and CSS. If you decide to use this option, please keep in mind that Lightspeed cannot provide technical support for it.