Thank you for your post & my apologies for the delayed response.
When creating a roof that has different walls heights you normally need to create faces at the different heights and then merge/join them into each other. There are a few tutorial videos in the link below which explain this in more detail may help with the issue you're having.https://www.youtube.com/playlist?list=PLNRcN-A1tOEz3iu9YZ1H0lSyiKzcSM9qF
If you're still unable to get the roof to work after watching the tutorials, would you be able to please send the model to email@example.com
so I can have a look at it? Thank you in advance.