How to set up a convenient, per-user and pretty secure SFTP server on 14.04 LTS

I'm currently setting up a future web server and now that my AMP are configured, I'd like to provide access to the web developper.

Coming back from a pretty long sleep, I discover that FTP seems pretty outdated...
From what I read everywhere, it seems FTP over SSH (sftp) is now the thing.
Following several miscellaneous howtos and tutorials, I managed to make it possible for the system-registered users to access the filesystem using an sftp client (filezilla in this case).

Althought that being great, I am not convinced that using system recognized users is really secure: I previously had several FTP server and always used specific virtual users with per-user virtual root dir and stuff.

• Do I really have to use system users & group for sftp?
• Is there any way to have per-user settings? (user "joe" fake root would be in /etc/www, user "bob" in /home/ftpdir/bob, all being members of ftpgroup, none having access to the shell or the other users' directory)?
• Which sftp should I use? I'm not even sure which one I am currently using...
  I think it's the system-provided one, (
  root@servername:~# which sftp /usr/bin/sftp
  ) and internal-sftp is in my sshd_config, but I have openssh installed and maybe I'm not using the "right one"?
• I am logged in from a windows machine through PuTTY in ssh and from several machines through X2go, all these as root (currently the only user with a shell access), for configuration purposes. I guess that commenting the PermitRootLogin from sshd_config will lock me out... So how can I securely access to my shell as root (I am aware that logging in as root is not recomended)?
• Is there, by any chance, a suitable GUI frontend for configuring / monitoring the server? I have been using PureFTP on several linux servers and found it pretty convenient. Not that I don't like console, but why use lynx when you can run firefox...