The Navigation tab allows you to change how the left navigation pane will look to students.
This can be done by dragging and dropping the different sections around or by clicking on the gear and then Move. From there, you choose between putting that page before or after a different page.
You can move the sections up and down the menu as you wish, creating a unique menu system specific to your course.
To hide a page from students, drag and drop them into the section at the bottom where they will be grayed out and labeled as "Page disabled, won't appear in navigation". Or click on the gear and hit X Disable.