Hello,
This is the default menu position provided with the Template. Your "default" menu will always be published here unless you have selected "No Menu" in the Template Manager under Menu. The menu you are using on the side is not the default area of this but there is not reason you cannot use this position.
There are no module positions above the "breadcrumbs" position as the "menu" block is not designed for modules, just the S5 Flex Menu system. You can review the layout of the modules here:
http://shape5.com/demo/vertex/index.php/features-mainmenu-47/template-features/94-module-positions