I'm assuming you created FTP / SFTP / Shell users. To confirm the users have been setup on the system, try logging into FTP / Shell as those users. If you can but they still don't appear on the Manage Users page, contact support. If FTP / Shell doesn't work, see if you created a mailbox-only by mistake on Manage Email page.
There is no such thing as a root FTP account. Each user on the system, including the mailbox-only users, get a home directory that is separate from that of other users. The first user you have is just that: the first.
You do not have a "super user" either. If you need to manage files owned by another user on your plans, simply login as that user. If you are up to it, check out using Unix Groups and permissions.
For FTP protocol, users are chroot'ed to their home directory. However SFTP is not.
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