I do similar although i add in a variable before calling the header include so i can include things in the header for specific pages.
<?php $addcode = '//whatever script or style you want here';?> <?php include_once('header.php'); //output the $addcode variable into the head after everything else?> <?php include_once('navigation.php'); ?>// Then the page html code goes here
<?php include_once('footer.php'); ?>`That way i can override the main CSS or add in code for a map or anything else that needs to be in the <head> section. You can either do this on a page by page basis or i have it built into my cms and just have the $addcode generated from the record being called.
hth