Did you originally install SS in that subfolder or did you move it there? The installer should pick up the fact it is in a subfolder and adapt the base url accordingly. So if you're moved into a subdir it could be that SS still thinks its in the root.

How do you mean you need to be able to access the root directory? If you installed SS in a subfolder then it should leave anything in that root folder alone.

The installation directly in to directory cms doesn't allow me to edit pre existing (both htm & php) files created using dreamweaver. I cannot get it to recognise that I want to work on content outside of the cms directory on pre existing files. It just creates the four workable files for the my site directory (I think thats where the files are stored). Ultimatly the client needs to use silver stripe to ammend content etc on pre existing silver stripe installation, thus giving them the ability to manage the content that's pre existing, then saving it to the orgininal location. Can silver stripe do this?