The Domino server Controller is a java based application that (among many other cool things) allows you to start and stop Domino server remotely without being disconnected like you would if using the remote Console from the Administrator Client .
Since the Controller runs as a separate java application it doesn't quit when the Domino server does. Your server commands are issued to the Controller and the Controller issues them to Domino to start, restart and stop it. There are a lot of other cool things you can do when running Domino under the Controller and using jconsole, but for now, here's how to go about setting it up.
Start the Registry Editor.
HKEY_LOCAL_MACHINE -> System, CurrentControlSet -> Services -> Lotus Domino Server -> ImagePath
Double Click on ImagePath and add the -jc switch to the end of the string