You can add jQuery and your own Javascript files and also style sheets by adding the necessary commands at the top of the file where you need to use them, as in the following example:
<HTML>
<head>
<?php
defined('_JEXEC') or die;
JFactory::getDocument()->addStyleSheet(JURI::root().'/tmpl/default.css');
JHtml::script(JURI::base() . '/tmpl/jquery-ui-1.10.3.custom.js');
JHtml::_('jquery.framework'); // load jquery
JHtml::_('jquery.ui'); // load jquery ui
JHtml::script(JURI::base() . 'tmpl/sample.js');
</head>
<body>
<!-- Remainder of your page content would go here -->
</body>
?>
I have found that sometimes Joomla is sensitive to the order in which things are loaded but a little experimentation generally solves the problem.