You have to be comfortable messing with wordpress. If you go into the theme folder and read the function.php file, you will find information on the menu system. If you google those terms, you will find what you are looking for. The latest version of wordpress comes with custom menus already in place. All you need to do is register new menus in the functions.php file, then place those menus in the theme code. So then when someone makes the primary menu, they get the menu on top and when they make the secondary menu, it gets placed wherever you put it. If you want it under the primary menu, then you place it there in the theme file.
Read the codex along with the code in the function.php, you can see how they did it
http://codex.wordpress.org/Function_Reference/register_nav_menu
Here is a nice tutorial showing how to register a new menu and place it in a theme
http://bavotasan.com/tutorials/wordpress-3-checking-out-the-new-menu-system/
in the end, to learn more, google – how to register wordpress menu
