To sum up:
- The user instance stuff with
--useris intended to be used on a desktop computer. Syncthing starts when you log in to gnome or something; and it stops when you log out. - The system instance stuff is useful for a server. Syncthing then starts during the normal bootup sequence and stays running. To be able to specify the user, there is the templating stuff with
@, e.g.:systemctl start syncthing@hans.service. - The user units are located in
/usr/lib/systemd/user/and can be overwritten in/etc/systemd/user/and~/.config/systemd/user/. - The system units are located in
/usr/lib/systemd/system/and can be overwritten in/etc/systemd/system/.
So, when you mix them up by accident, strange things happen.
Note: The paths are valid for arch linux and fedora and are documented in the systemd manpages. Debian (as usual) does its own thing.