Have you tried adding this to the themes functions.php?
function add_supersubs() {
wp_enqueue_script('superfish', get_stylesheet_directory_uri() . '/js/superfish.js');
wp_register_script('supersubs', get_stylesheet_directory_uri() . '/js/supersubs.js','superfish');
wp_enqueue_script('supersubs');
}
add_action('wp_enqueue_scripts', 'add_supersubs'); //
this assumes the supersubs.js is in the js folder of the main theme directory.
You’ll also need to modify the header js to fit supersubs.