Here is how this digital surgery would work for CSS. You need to tell the server two things: first, to parse CSS files for PHP commands, and second, to send the correct MIME type. Add the following lines to your httpd.conf file for Apache:
AddHandler application/x-httpd-php .css
header('Content-type: text/css');
Next, you can merge your CSS files together with PHP inside the CSS file, like this:
<?php
include("layout.css");
include("navigation.css");
include("advanced.css");
?>