Drupal allows multiple menus to be created but it starts with a default Main Menu. This is the primary menu for the site that all content types can be added to (unless otherwise specified).
The Main Menu sits in the black Top Menu region and is the primary navigation for the site. It allows a single drop down level.
The vertical menu in the Sidebar Second region uses the Main Menu as well but starts at the second menu level down and shows another level of child page under the current on. It is contextual to the section of the site the user is in, showing the current page, its siblings and its children.