Please take a look at this video.
Copy the Raphuccino folder to your project’s Frameworks folder and include
@import <Raphuccino/Raphuccino.j> in your class/controller/whatever.
Then create your RCRaphaelView as you would create a normal CPView, or use Atlas and a custom view and set it’s class to RCRaphaelView.
The code is commented very well and the demo project and the RaphaelJS docs should cover the rest.