Drupal - Add external javascripts
In your theme's template.php file use drupal_add_js() to the page preprocess method (or an equivalent preprocess).
function hook_preprocess_page(&$vars) {
drupal_add_js('http://cdn.jquerytools.org/1.2.6/jquery.tools.min.js', 'external');
}
The method of adding javascript depends on for what you are adding javascript for. There are different ways to add js.
By defining in the theme.info file.
Adding it inline.
Adding an external js file.
You can add a js info file with this simple line of code
scripts[] = js/myscript.js
Or you can use the php function provided by drupal drupal_add_js
This functions lets you easily add a JavaScript file or helps in setting an inline code to any page in your theme and it takes 5 parameters (you see it in the api reference).
There is an detail post on this here.