Adding website template around PunBB

I am in the process of cusomising PunBB to match the website colours.  Once I have done this, I would like to add the header and footer of the rest of the website so the full website menu can be seen around PunBB.  Any ideas of how best to do this?  I have tried adding it to footer and header, but that caused some problems with the search and index.
Would I be best to put it in an iframe? 
Or do I customise the style to add the header and footer? 
The rest of the website puts the page content into the template page which is loaded on the web.  Code goes like this:

<?php
$base_dir = '.'; // base dir is the main directory for the website
include_once $base_dir."/config.php";

// connect to database

database_connect();
$content = 'text';
$title = 'Welcome';
$head = '';
$login = login_details();

make_page($content, $title, $head, null, $links);

?>

Can I put PunBB into this script?