Root Folder Problem in CS4

I have an old site I support with dreamweaver CS4. The site seems to have a root folder problem. The links have seemed to have all changed to my document folder and I keep getting an error message that the files aren't in my root folder, but they definitely are.  I am wondering how I can make sure that the links point to the root folder and not my documents folder. 

How can I change my root folder. Also should the root folder set up, should the links be relative to the document or site root?

The site is very old, and is getting buggy. I am trying to convince the group to upgrade!!!

Thank You in advance for any help.