Overcoming a duff document_root

The hosting platform I'm about to deploy Perch onto doesn't resolve the document_root path to the root folder of the site. It points to the root folder of the server a few levels above (don't ask why - they can't tell me).

The hosting company have advised to change the Perch CMS.

Is there a best practice to follow here to ensure new pages are created correctly and files/images are uploaded correctly?