I have been learning syntax for PHP and practicing it. I come from a .NET background so masterpages always made things pretty easy for me when it came to headers and footer
What you're doing is ok until you start using "Views" or "Templates" in which case you no longer arrange your content HTML inside the "controller" or "action" running.
Instead you will load a view and populate it with values which leaves all the HTML source ordering to the view and not your PHP file.
$view = new View('layout.php');
$view->header = $header;
$view->content = 'This is the main content!';
$view->footer = $footer;
print $view;
which then loads the layout file which looks something like this:
...