How do I include jQuery scripts at the bottom of the  tag?
The example on the documentation for drupal_add_js() can explain this.

drupal_add_js('jQuery(document).ready(function () { alert("Hello!"); });',
  array('type' =&gt; 'inline', 'scope' =&gt; 'footer', 'weight' =&gt; 5)
);


If you want to add jQuery files, just change 'type' to 'file'.