Menus and Blocks are the central elements used to build a navigational structure. A Menu is a collection of links; Blocks have many uses, but for this discussion we will focus on how they are used to display menus.
At its most basic, designing a navigational structure can be reduced to this simple process:
Create a list of places that you want your users to go, and/or of things they will need to do. For example, you want your students to be able to see a list of assignments, your blog, and other student blogs; you could place links to these pages in a custom menu, which would automatically generate a block.
Then, via the block display settings, show the block.