Hmm, definitely kind of a tough one.
You can place the secondary navigation into the main navigation container with something like this:
add_action('after_setup_theme','generate_float_navigation_below');
function generate_float_navigation_below()
{
remove_action( 'generate_before_header_content', 'generate_add_navigation_float_right', 5 );
remove_action( 'generate_before_header', 'generate_add_secondary_navigation_before_header', 7 );
add_action( 'generate_after_header_content', 'generate_add_navigation_float_right', 5 );
add_action( 'generate_inside_navigation', 'generate_add_secondary_navigation_before_header', 7 );
}
That would place the secondary navigation (if set to before header) inside the main navigation, above it.
Let me know if that gets you closer 🙂