look at my last 2 posts here:viewtopic.php?f=52&t=4867&p=31902&hilit=upstart#p31902
upstart has replaced init, but upstart is not fully featured yet so there is some legacy stuff still.
there is really only one run time level now "rc2.d", but the rcN stuff is legacy stuff and has been left in for simplicity, maybe.
upstart is event based so try to forget run levels and think events. eg: reboot, startup, run, halt.
you can also check out:http://upstart.ubuntu.com/