Your tips are spot on. I made a small change to allow for adding new links using the Link Manager from Wordpress.

/* Add the top navigation menu */
/* Links for top menu will need to be manually added here, since this menu isn’t supported by Thesis */
function topnav_menu() {
?>

<?php wp_list_bookmarks( 'title_li=&categorize=0&category=3&before=&after=&show_description=0&orderby=url’ ); ?>

<?php
}


/* Add the top navigation menu */
/* Links for top menu will need to be manually added here, since this menu isn't supported by Thesis */
function topnav_menu() {
?>

<?php
}