My PHP files in my root directory INCLUDE header.php. Header.php INCLUDEs functions.php. I\'m adding new pages in a subdirectory, so I added leading slashes to all my links
Include and Require literally pull the code into the executing file, so one thing to watch out for is that the files in a subdirectory are running from the working directory.
Example:
|-templates-|-header.php
Docroot--|
|-inc-|-functions.php
|
|-index.php
Index.php
template/header.php
because the header.php code is being executed from the docroot due to the include.