The File Upload option that is presented when you click on File Manager from the Left Navigation in the CNC is limited to Top level directories in your /big/dom/xdomain and /big/dom/xdomain/www directories.
Subdirectories of those will not be listed as in some accounts the listing would possibly 100's if not 1000's of directories.
would be listed but
I hope this helps clarify.
Note a far more efficient method of uploading files would be to use a standard FTP client such as Core FTP (my personal favorite)