I have a Drop down mega menu using a CSS file and a HTML file.    I want to use this instead of the drupal primary menu.   I have been advised to change the HTML in the page-header.inc file but I don't know how to do this?

On looking at the page-header.inc file, do i place the code under the file or in the header?   I have no idea! Do I have to change this section?   

<?php if (isset($primary_links)) : ?>
    <?php print theme('links', $primary_links, array('class' => 'links primary-links')) ?>
  <?php endif; ?>

any advice would be great, I'm a noob