Can I tell NcFTPd to authenticate users from both the system password file and a NcFTPd password database?
Yes. The passwd line in the domain.cf is comma-delimited, with each token being one password file to check. NcFTPd will check the files in the order you list them, so if you have passwd=/etc/passwd,/etc/ftppasswd.db, then a user in /etc/passwd would take precedence over a user by the same name in /etc/ftppasswd.db.