To create the menu of your website go to WordPress menu > Apparence > Menus and create a new menu. The left area show you all the possible menu items that you can insert in your menu, the right area is your final menu, you will add the items by drag and drop the items of left area to the right area. When you are done and all the menu items are in the right area you can save the menu by click on blue button Save menu.
To set the menu as main menu, the menu usually placed on top of your website, select Header Menu on Menu settings box on bottom. To set the menu as footer menu, the menu usually placed on bottom of your website, select Footer Menu on Menu settings box on bottom.
To set the menu as secondary top menu of main menu, the menu usually placed on top of your website, before the main menu, select Top Menu on Menu settings box on bottom, top menu area must be activated from WordPress menu > Apparence > Theme options > Menu. Go to HTML documentation for live preview and advanced customizations.