If you do things the way that jatark outlined in the post I linked to, linking to the template should be quite easy. For example, you could do something like this:
template.php - lives in the root directory
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<title><?=$title ?></title>
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<meta name="keywords" content="<?=$keywords ?>">
<meta name="description" content="<?=$description ?>">
<style type="text/css">
</style>
</head>
<body>
<div id="header">
</div>
<div id="content">
<?=$content ?>
</div>
<div id="footer">
</div>
</body>
</html>
webpage.php - this can live anywhere
<?php
$title = 'This is a title';
$keywords = 'these, are, some, keywords';
$description = 'this is a description';
$content=<<<EOF
<p>This is some content.</p>
EOF;
include_once ( '/var/www/htdocs/template.php' );
?>
As you can see, it doesn't matter where your file resides, the path to the template will always be the same. I hope this helps.