I think I have figured it out.
include "/include/footer.php"; // does not work
include "include/footer.php"; // DOES work
include "../include/footer.php"; // DOES work
I just do not understand why the way I originally had it does not work. It seems like the way to access the files. You do not have to worry about it being ../ or ../../ or whatever because you can start from the webroot no matter where the page that is making the include call is located.