If you are managing a remote site, web server that you do not have direct access to (terminal or ssh) and you have to do it with cpanel, then I know how much pain it is. I had the same issue until recently when I discovered <a href="http://http://www.manyfish.co.uk/sitecopy/" target="_blank">sitecopy.
Description of sitecopy:
sitecopy allows you to easily maintain remote Web sites. The program will upload files to the server which have changed locally, and delete files from the server which have been removed locally, to keep the remote site synchronized with the local site, with a single command.