If I understand, you want to have a single header file, but have the parts of it (meta) change depending on the page.
That's easy. Just define the variables before you call the include. So page might look like:
<?php
$meta_description = "blah";
include("header.php");
//more content here
?>
and the header.php might look like:
<html>
<head>
<?php
echo("
<meta description:$meta_description>
");
?>
</head>
(I know the <meta> format is wrong, but you get the idea).
This way, anything that changes, like the title or meta, are defined in the page, and passed to the header.