Adding js to Drupal 6

open a file name external-js.tpl.php and add the script with a script tag of the external js script

<?php
<script type="text/javascript" src="http://www.google-analytics.com/urchin.js"></script>
?>

in template.php

<?php
function Nefertari_preprocess_page(&$vars){
$path = drupal_get_path('theme', 'Nefertari');
$vars['external_js'] = theme_render_template($path.'/external-js.tpl.php', $vars);
$vars['footer'] .= '<script type="text/javascript">    _uacct = "UA-GOOGLE-ID"; urchinTracker(); </script>';
}
?>

source