Create the walls and roof elements that make up the dormer.
Revit roof dormer.
Create the dormer roof and join it to the main roof.
After adding a dormer cut an opening for it through the roof.
Use the join roof tool to join the dormer roof to the primary roof.
Move the walls to the dormer.
Select the wall type and constraints for a dormer that will be added to a roof.
Use the modify sub elements button to select your newly placed points.
Do not use the join geometry roof tool for this task or you may encounter an error when creating the dormer opening.
This video demonstrates the following.
Select your flat roof press the modify sub elements button that appears.
Add point or split line if better suited creates points at intersections place your new points as required.