PowerCMS cannot automatically generate the correct path for you in this case, you will need to adjust the path accordingly.
For example, if you powerCMS is Located at:
CMS/
and you have a page at:
subfolder/
you will need to manually adjust the paths to move down two directories to the root, then find the CMS folder:
<?php include "../../CMS/Connections/localhost.php"; ?>
<?php include "../../CMS/WA_CMS/WA_CMS.php"; ?>
If you have another page at:
subfolder/
the paths will need to be adjusted to move down 4 directories to the root, then find the CMS folder:
<?php include "../../../../CMS/Connections/localhost.php"; ?>
<?php include "../../../../CMS/WA_CMS/WA_CMS.php"; ?>