You can add these CSS blocks to your Thesis -> Custom CSS screen

1. Hide the top primary menu:

#top-area {display: none;}

For the secondary menu you can use:

#subnav {display: none;}

You can also use the Thesis Skin Editor to remove the menus all together from the various templates.

2. Customize sub nav colors:

#subnav {background: #000;} /* Overall menu background */
#subnav li a:hover {background: #fff; color: #ff0000;} /* Hover background / text color */
#subnav li a:active, #subnav .current-menu-item a, #subnav .current-cat a, #subnav .current_page_item a {background: #333;} /* Current active menu item color */
#subnav li a {border-right: 1px solid #ff0000; color: #ff0000;} /* Border & default menu text color */

2. Customize footer area colors:

#footer-widgets {background: #000;} /* Footer widget area background color */
#footer {background: #fff;} /* Area with copyright info background color */