Codeigniter CSS and Javascript files usage
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I am writing a webpage with CI.I use the latest version.  I need to learn how to imply CSS and Javascript files. I use nivoslider , jquery and many css files. I use application directory as

    +application
      +views
        +pages
         -home.php
        +templates
         -header.php
         -footer.php
    +system
    +user_guide. 

Can you explain how to enable js and Css files. I made a research but my mind is blown away with the versions of codeigniter. 
this is my header.php 

    <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN""http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
    <html xmlns="http://www.w3.org/1999/xhtml">
    	<head>
    		<title>Kırmızı Eğitim Merkezi</title>
    		<meta name="description" content="Empire - XHTML Template" />
    	<!-- CSS -->
    	<link href='./fonts/sansation.css' rel="stylesheet" type="text/css" />
    	<!-- Get any font from here easily: http://www.google.com/webfonts -->
    	<link href="./css/style.css" rel="stylesheet" type="text/css" />
    	<link href="./fancybox/jquery.fancybox-1.3.4.css" rel="stylesheet" type="text/css" />
    	<link href="./css/nivo-slider.css" rel="stylesheet" type="text/css" />
    
    	<!-- UPDATE BROWSER WARNING IF IE 7 OR LOWER -->
    	<!--[if lt IE 8]><link href="css/stop_ie.css" rel="stylesheet" type="text/css" /><![endif]--><!-- JAVASCRIPTS -->
    	<script type="text/javascript" src="./js/jquery.min.js">
    	</script><script type="text/javascript" src="./js/jquery-ui-1.8.17.custom.min.js">
    	</script><script type="text/javascript" src="./fancybox/jquery.fancybox-1.3.4.pack.js">
    	</script><script type="text/javascript" src="./js/jquery.nivo.slider.js">
    	</script><script type="text/javascript" src="./js/jquery.bgslider.js">
    	</script><script type="text/javascript" src="./js/preloader.js">
    	</script><script type="text/javascript" src="./js/farbtastic.js">
    	</script><script type="text/javascript" src="./js/basic.js">
    
    	</script>

Can you advice me a way to use them ?