The Menu Links section is where you add links to the menu of your website.
The main menu goes across the top of the site below or beside the header (option of placement when editing your theme).
Top Mini Menu
This menu is shown at the very top of all pages, above the header and everything. This is generally where you want your cart, checkout, account links.
Side Bar Menu
You have the option to use a side bar on your pages when editing your theme. If using a side bar, this side bar menu can be added to it when editing the Side Bar section.
Adding links to the menus
There are 2 ways you can add links to the menus.
1) Click the Add Link tab while in the Menu Links section. There you can either select from an existing section or top level page or enter in the URL you want the link to go to.
2) When in the Site Content area, the left side of the page lists the sections you have created. Click the +menu link under the section name to add it to the menu. Same with top level pages. When viewing the list of top level pages, click the +menu link under the page name.
Rearranging the link order.
Simply drag and drop the links to change the display order.