Systemd flipped this all around, and now instead of just changing files, you have to use applications to specify changes to your system. Want to stop something from starting? Well, it used to be that you just move it out of the init directory...

Enable and disable just create symlinks of the "just changing files" files in your example. It tells you this every time you install something that enables a service.
Want to do it manually? ln -s (or rm the link to "disable" it).
Want it to happen later in the init sequence? Put the link in a different .target directory.
All "systemctl enable" does is put the symlink in the target directory that's specified in the Install section of the unit file.

As for "specifying a service"... Everything is a unit file (yes, file), journalctl -u just means "only show me logs for this unit".
There's no flag for "specifying a service", you just type in the service name. If there's any ambiguity (eg. unit.service and unit.socket), you type the service name followed by .service
A flag you might find useful is -g, which means "grep for this string". You can combine this with -u to narrow it down.