Becoming Agile: Click Once deployment using NAnt.
Great example of how to Create an initial ClickOnce application deployment package using Mage.exe, then perform update Mage.exe builds to update the Application manifest and resign the Deployment manifest.
Solid explanation… Short and sweet. Though you might not need the NAnt retoric. The key is understanding the Mage.exe steps being taken. You translate the NAnt into MSBuild if you would like.