I think you may have missed the point of PHP a little...
CSS is purely for display - nothing more, nothing less.
PHP is a programming language, that can do - well just about anything really! From something as simple as a dynamic date, to 'including' files (such as your navigation), all the way up to complex calculations and functions (ecommerce systems, user profiles, anything your imagination can come up with).
In your example, you might have a PHP container page (index.php) with calls for your navigation, body, footer, etc. You would then use CSS to format the display of the page.
If you need any more clarification on anything, ask