How can i seperate jQuery code from my html markup
<p>Am using php to develop an app and i created a simple template system for headers and footers.
My dilemma is that i have many views that depend on the jQuery code, and they all user the header template. Here an excerpt from the header. </p>

<pre><code>&lt;!DOCTYPE html&gt;
&lt;html&gt;
&lt;head&gt;
&lt;meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /&gt;
&lt;title&gt;NgInformr | Adminstration | &lt;?php if(isset($title)) { echo $title; }?&gt;&lt;/title&gt;
&lt;?=$html-&gt;js("javascripts/top_up")?&gt;
&lt;?=$html-&gt;css("admin-css")?&gt;
&lt;?=$html-&gt;css("form-style")?&gt;
&lt;link href="http://localhost/nginformr/www_root/js/uploadify/uploadify.css" type="text/css" rel="stylesheet"/&gt;
&lt;?=$html-&gt;css("base/jquery.ui.all")?&gt;
&lt;?=$html-&gt;js("uploadify/jquery.uploadify.v2.1.4.min")?&gt;
&lt;?=$html-&gt;js("uploadify/swfobject")?&gt;
&lt;?=$html-&gt;js("jquery-ui-1.8.9")?&gt;
&lt;?=$html-&gt;js("jscripts/tiny_mce/jquery.tinymce")?&gt;
&lt;script type="text/javascript"&gt;
$(document).ready(function() {
//Uploader
$('#file_upload').uploadify({
    uploader : "/nginformr/www_root/js/uploadify/uploadify.swf",
    script  : "/nginformr/www_root/js/uploadify/uploadify.php",
    folder : "/nginformr/www_root/uploads",
    auto : true,
    onComplete : function(event, queueID, fileObj, reponse, data) {
        $('#file_details').css({display:"block"});
        $('#path').val(fileObj.filePath);
        $('#type').val(fileObj.type);
    },
    onError    : function (event,ID,fileObj,errorObj) {
      alert(errorObj.type + ' Error: ' + errorObj.info);
    }
});
$("#side_menu").accordion({header:"p",fillSpace: false});
//Ajax for select boxes
$('#state').change(function() {
        $('#city').html("");
        var id = $('#state').val();
        var dataString = "id="+id;
    $.ajax({
        url:"http://localhost/nginformr/cities/ajax_cities",
        type:"POST",
        data:dataString,
        success:function(html) {
            $('#city').append(html);
        }
    });
});
$("#city").change(function() {
    $('#area').html("");
    var id = $('#city').val();
    var dataString = "id="+id;
    $.ajax({
        url:"http://localhost/nginformr/areas/ajax_areas",
        type:"post",
        data:dataString,
        success:function(html) {
            $('#area').append(html);
        }
    });
});
$('#sector').change(function() {
    $('#category').html("");
    var id = $('#sector').val();
    var dataString = "id="+id;
    $.ajax({
        url:"http://localhost/nginformr/categories/ajax_categories",
        type:"post",
        data:dataString,
        success:function(html) {
            $('#category').append(html);
        }
    });
});
$(".widget").draggable();

//TinyMCE Editor
$('textarea.tinymce').tinymce({
    // Location of TinyMCE script
    script_url : 'http://localhost/nginformr/www_root/js/jscripts/tiny_mce/tiny_mce.js',

    // General options
    theme : "advanced",
    plugins : "pagebreak,style,layer,table,save,advhr,advimage,advlink,emotions,iespell,inlinepopups,insertdatetime,preview,media,searchreplace,print,contextmenu,paste,directionality,fullscreen,noneditable,visualchars,nonbreaking,xhtmlxtras,template,advlist",

    // Theme options
    theme_advanced_buttons1 : "save,newdocument,|,bold,italic,underline,strikethrough,|,justifyleft,justifycenter,justifyright,justifyfull,styleselect,formatselect,fontselect,fontsizeselect",
    theme_advanced_buttons2 : "cut,copy,paste,pastetext,pasteword,|,search,replace,|,bullist,numlist,|,outdent,indent,blockquote,|,undo,redo,|,link,unlink,anchor,image,cleanup,help,code,|,insertdate,inserttime,preview,|,forecolor,backcolor",
    theme_advanced_buttons3 : "tablecontrols,|,hr,removeformat,visualaid,|,sub,sup,|,charmap,emotions,iespell,media,advhr,|,print,|,ltr,rtl,|,fullscreen",
    theme_advanced_buttons4 : "insertlayer,moveforward,movebackward,absolute,|,styleprops,|,cite,abbr,acronym,del,ins,attribs,|,visualchars,nonbreaking,template,pagebreak",
    theme_advanced_toolbar_location : "top",
    theme_advanced_toolbar_align : "left",
    theme_advanced_statusbar_location : "bottom",
    theme_advanced_resizing : true,

    // Example content CSS (should be your site CSS)
    //content_css : "css/content.css",

    // Drop lists for link/image/media/template dialogs
    template_external_list_url : "lists/template_list.js",
    external_link_list_url : "lists/link_list.js",
    external_image_list_url : "lists/image_list.js",
    media_external_list_url : "lists/media_list.js",

    // Replace values for the template plugin
    template_replace_values : {
        username : "Some User",
        staffid : "991234"
    }
});
});
&lt;/script&gt;
&lt;script type="text/javascript"&gt;
  TopUp.host = "http://localhost/nginformr/";
  TopUp.images_path = "www_root/img/top_up/";
&lt;/script&gt;
&lt;/head&gt;
&lt;body&gt;
&lt;div id="header"&gt;&lt;!-- ------Header --&gt;
&lt;div id="logo"&gt;
&lt;a href="./"&gt;&lt;?$html-&gt;img("nginformr_logo.png") ?&gt;&lt;/a&gt;
&lt;/div&gt;

&lt;div id="user_controls"&gt;
&lt;?=$html-&gt;link("admin/users/logout","Logout")?&gt;
&lt;/div&gt;
&lt;/div&gt;
</code></pre>
