JavaScript and images files are not recognized

You need to give the full path to your theme files. To get the URL of your theme, use the WordPress function bloginfo( 'template_directory' ); so at a minimum you would need:

<script src="https://wordpress.stackexchange.com/questions/18828/<?php bloginfo("template_directory' ) ?>/jquery.js" type="text/javascript"></script>

However, scripts / styles should really be “enqueued” using wp_enqueue_script(); (see http://codex.wordpress.org/Function_Reference/wp_enqueue_script)

I would recommend taking a look at some other themes to see how they include thetheme files like this. Also the Codex page on Theme Development is a good place to start: http://codex.wordpress.org/Theme_Development

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