Okay, the Autofocus author, Allen Cole, was kind enough to quickly respond and point me to the following forum post:
http://themeshaper.com/forums/topic/a-better-way-to-use-the-new-menu-in-wordpress-30-final-version
The complicated one at the beginning works (and not the later simpler version posted by @em hr which is what I tried).
So, all I did to get WP 3 Menus to work is open functions.php in the autofocuspro theme folder and paste the following as the last item above the closing ?> string:
// We declare that our theme supports wp_nav_menu()
add_theme_support( 'nav-menus' );
// We Register the a new menu for the theme called "Primary Menu"
function register_primary_menu() {
register_nav_menu( 'primary-menu', __( 'Primary Menu' ) );
}
add_action( 'init', 'register_primary_menu' );
// We remove the standard Thematic menu
function remove_menu() {
remove_action('thematic_header','thematic_access',9);
}
add_action('init', 'remove_menu');
// We create the new wp_nav_menu called "Primary Menu" in our theme
function new_access() { ?>
<div id="access">
<div class="skip-link"><a href="#content" title="<?php _e('Skip navigation to the content', 'thematic'); ?>"><?php _e('Skip to content', 'thematic'); ?></a></div><!-- .skip-link -->
<?php /* Our navigation menu. If one isn't filled out, wp_nav_menu falls back to wp_page_menu. The menu assiged to the primary position is the one used. If none is assigned, the menu with the lowest ID is used. */ ?>
<?php wp_nav_menu( array(
'theme_location' => 'primary-menu', // we define this as being the previously registered "Primary Menu"
'menu_class' => 'sf-menu', // we assign the sf-menu class to the menu ul so that superfish workds
'container_class' => 'menu' // we assign the menu class to the menu container div so to keep it compatible with the Thematic menu styling
));
?>
</div><!-- #access -->
<?php
}
add_action('thematic_header','new_access',9);
Remember that updates to the child theme from the author will overwrite any changes made!