Example function of how to set the order of posts for an archive or taxonomy--specifically for a custom post type, but can be used anywhere posts are listed, such as a specific category/taxonomy.

simple-staff-order.php

<?php

/*
 * This function is part of Simple Staff for Genesis. Extracted for educational purposes. Could be used also
 * in a theme's functions.php file, if you're not working with a plugin. Do not include the opening tag.
 */

add_action( 'pre_get_posts', 'simple_staff_order', 9999 );
function simple_staff_order( $query ) {
	if ( $query->is_main_query() && ( is_post_type_archive( 'staff' ) || is_tax( 'department' ) ) ) {
		$query->set( 'orderby', 'menu_order' );
		$query->set( 'order', 'ASC' );
		$query->set( 'posts_per_page', -1 );
	}
}