The Cpanel branding feature is very simple to use . Simply place an image called cp.gif, cp.jpg, or cp.png in the folder in your home directory called /cpanelbranding/bluelagoon. (full path to directory is /home/username/cpanelbranding/bluelagoon) Once you place an image there, it will replace the 'cpanel' image at the top of your users' cpanel. That's all there is to it.
At the time of writing, the Bluelagoon theme is the only one that supports this feature. However, we do expect others, specifically the X skin, to follow shortly.