Positioned fixed header and the middle part content issue

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CSS

HTML

jQuery

I have the flowing issue:
-------------------
header||||||||||||||||||
-------------------
content|||||||||||||||||
-------------------
footer||||||||||||||||||||
-------------------

The header and footer are positioned fixed.
the content part(divided to sections) is very long(each "section" is 5000px long).
I am trying to do a site with navigation that instead of post back when clicking a "page"
in the navigation and load other page.
Will only animate with jquery and 'slide' down to the requested section.

I am having trouble with the position fixed header, each time I slide to different section
,the header hiding the content(and i understand why - it's calling the page id and then go to that height, not knowing of the header) what I need to do is always set the 'top' so the content page will be under the header.
I thought that if I'll set the position of the class page to relative and set the top to some pixels it will be ok ( cause i thought that if I position element to absolute,fixed,relative the top considered to be from the widow it self), isn't it?

This is the navigation html:

<div id="header" class="shadow">
            <ul id="nav">
                <li><a href="#section1"></a></li>
                <li><a href="#section2"></a></li>
                <li><a href="#section3"></a></li>
            </ul>
        </div>

Header style:

#header {    
    height: 20%;
    width: 100%;
    position: fixed;
    background: #F5F6F7;
}

'section' style(one long page separated to sections)

.section {
    top: 163px;
    height: 5000px;
    width: 100%;
    position: relative;
}

jQuery part:

$('#nav a').bind('click', function (event) {
               var $anchor = $(this);

               $('html, body').stop().animate({
                   scrollTop: $($anchor.attr('href')).offset().top
               }, 1500, 'easeInOutExpo');

               event.preventDefault();
           });

Am I approaching that solution the right way?
Thanks, I hope it make sense