Select your flat roof press the modify sub elements button that appears.
Revit roof dormer.
Create the roof opening and finish the dormer.
Use the modify sub elements button to select your newly placed points.
Create the dormer roof and join it to the main roof.
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.
Move the walls to the dormer.
Use the join roof tool to join the dormer roof to the primary roof.
Create the walls and roof elements that make up the dormer.
To use this do the following.
Add point or split line if better suited creates points at intersections place your new points as required.