I have finally figured out how to create a cupola. I have created a youtube video on how to do it. You can find it at https://youtu.be/FlU4H5F8wE8
The key is when you build the roof you must make sure the auto-rebuild is turned off, and that you have already created the cupola. It's hard to explain it just in a brief paragraph and the video explains it much better. I'll do my best to answer any questions I can. I'm surprised that no one has figured this out as it is fairly simple once you get the hang of the concept. It did take me several hours, but I finally did it.