You can't use Software Update to install OS updates (you can update everything else through there though). It's fairly easy to install the updates via USB as long as you have your configuration and drivers backed up though.
That's good to know, might have to give that a shot next time. I've actively avoided doing it that way up until now since it's the standard recommendation not to. I just upgraded mine to 10.9.1 today from 10.8.5, by booting from a Unibeast USB stick - worked flawlessly.
