First of all we need to register our new menu:

// Register 'Primary Menu'
register_nav_menus( array(
 'primary-menu' => __( 'Primary Navigation' ),
 ) );

Next step will be to remove the old menu from Thematic and add the new one:

// Remove standard menu
function remove_menu() {
	remove_action('thematic_header','thematic_access',9);
}
add_action('init', 'remove_menu');

// Create wp_nav_menu
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>
			<?php wp_nav_menu( array( 'menu' => 'primary-menu', 'container_class' => 'menu', 'menu_class' => '', 'fallback_cb' => '' ) ); ?>
	</div><!-- #access -->
<?php
}
add_action('thematic_header','new_access',9);

And finally we need to add the needed UL class to support Superfish:

// Add the UL class to support Superfish
function wp_nav_menu_add_menuclass($ulclass) {
	return preg_replace('/<ul>/', '<ul class="sf-menu">', $ulclass, 1);
}
add_filter('wp_nav_menu','wp_nav_menu_add_menuclass');

Please keep in mind that WordPress 3.0 is still not final. This code might break at any time. Don’t rely on it!