You'll notice when editing a domain/subdomain it only lets you specify a single "FTP / CGI" user. This means whomever that user is, that is the only one that should login to FTP or shell to manage files for that domain.
Each file or directory is "owned" by a single user and group.
Each FTP/shell user has his own "home directory" in which to store his own files.
The web server is configured to look for web site files in a subdirectory of a single "home directory".
Only the "owner" of a file/directory gets to set permissions. If one is not careful, and attempts to have other users manage files or directories they don't own, then the permissions may prevent the web server, scripts and other services from functioning, and users will not be able to create, edit or remove files.
To solve your problem without causing headaches, you need:
1. Two FTP/shell users, "shared_one" and "shared_two" for example.
2. Set Domain1 FTP/CGI user to "shared_one"
3. Set Domain2 FTP/CGI user to "shared_two"
To manage files:
No matter whom the person is, the person needs to login as "shared_one" to manage Domain1, and "shared_two" to manage Domain2.
It's really that simple.
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