Use another folder on server as base folder

I am writing a content manager for my clients and I want to be able to access the content manager on a subdomain of their website. (ex: cms.thedomain.com -> http://www.thedomain.com). All the files sit on the same server, however 1 sits in a folder /www/thedomain.com/ and the cms sits in another folder /www/cms.thedomain.com/. Is there a way to setup FCKEditor to reference the main site's folder for upload/file manager, stylesheets, and images? Since FCKEditor has server side integration, i figured there was a way to accomplish this without major modifications.

This would need to modify the base HREF (so /img/photo.jpg actually points to http://www.thedomain.com/img/photo.jpg instead of http://cms.thedomain.com/img/photo.jpg)

And the file browser will browse the files in the other folder on the server. Thanks, and I love this editor!