Add custom php/js menu below header

Is there a way to add a dynamic menu (php,js) below the header so that it doesn't get overwritten with any updates? I've added to header.php, but I have a feeling its not the best solution.

<?php bfa_header_config($bfa_ata_configure_header); ?>
<?php require_once("../CSSMenuWriter/cssmw_content/menu.php"); ?>

Thanks to all, especially Flynn for the great customizable theme!