When you have an FTP or shell user, this user gets a "home directory" in which to store files, such as mail. When you setup a domain, you must specify a particular user so that the files for that domain will be located in a subdirectory of his home directory for the web server to use.
So if you have one domain, only one of your users will have access to the files used for the web site. If you have two, and you want user #1 to access domain #1 and user #2 to access domain #2, then you can do that by using the "Domains -> Web" panel to specifiy user #2 as the CGI user for domain #2, and then uploading the site files into the directory specified as "Web Directory" on that panel, given that domain #2 is fully hosted.
If you want two people to upload files for the same site, then they will need to either share the FTP login, or you can see if a web-based file management application would work for you.
If user #2 just need to upload files to a path on the site, ie http://example.com/user2/, then use the "Remap Sub-dir" option to map URI-path /user2/ to /home/user2/something
If the problem is that the directory specified for "Web Directory" doesn't actually exist, then create it.
Perl / MySQL / HTML+CSS