path reference problem after uploading image

I want users to be able to upload an image (or any media) along with their text. Then I need to be able to move/rename those files on the backend via php once they have saved their work. The uploaded image is stored in a dir just below the site root, but outside the fckeditor root dir. Once the image is uploaded to the server something changes because I can't access the server version using either relative or absolute paths. When I do a scandir('/') for the root, instead of getting the server root, I get the drive contents where the server is installed. I tried rebuilding the paths (both src and dest) using the fck function GetRootPath(), but this was not a sufficient work-around because I still can't move the files around I assume because I'm trying to manipulate the files using local file-system paths (c:\...), vs. relative paths (../../) (likewise with url-wrappers). I may not be using the correct terminology (not a server admin). So where did I go wrong here.

I made the necessary script adjustments as the wiki suggests and my fck upload config is as follows (both config files):
$Config['UserFilesPath'] = '/phenomRep/upload/userfiles/' ;
$Config['UserFilesAbsolutePath'] = '' ;

I wasn't sure what the second var should be so I left it blank. I didn't want to set it to a value/path specific to my dev machine, but maybe that's what's causing the problem. Can the second var take a url wrapper? Is there something else I need to do to be able to reference the uploaded files using relative paths?

Any help/comments appreciated. Thanks.