Well, you really don't want to be logging in as root to do anything but admin work. There are a few ways to set things up, depending on how you want to run things.
1) If you want to run the java window, you should install D2OL into your home directory. You can then probably put something in your bash_profile (or approriate file for your shell type) to start it up when you log in; otherwise, start it manually. You can also run the controller with the CLI flag if you don't want to be bothered with a bulky GUI.
2) If you want it to start on reboot, and to run as a 'service', then you probably want to to run the controller in file based mode, and start it in rc.local.