Hi,
I think this is more of a menu-issue in WP than in TT. You have to change your top menu to, let's call it Main, place the menu items you want, and save the menu. Then you go to the Location tab and select the Main menu as your theme location 'menu'. The other one (or 2, depending on how many sidebars you have chosen), is/are related to the vertical menus in sidebars.
Hope this helps.
Helen