It sounds like you just need to adjust the code from the developer comments to account for the cms folder. instead of adding
<?php include "Connections/localhost.php"; ?>
<?php include "WA_CMS/WA_CMS.php"; ?>
to the top of your page, use:
<?php include "cms/Connections/localhost.php"; ?>
<?php include "cms/WA_CMS/WA_CMS.php"; ?>