Assuming you already installed the Generate Roof plugin check out this topic describing dormers and integrating Velux windows:
https://www.sweethome3d.com/support/for ... ,190#60535
Don't forget to install the special window library Dorin created to integrate the windows in the roof.

That the roof is above 2 levels doesn't make a difference. After generating it's another object you can move to another level or give a different elevation. That way you should be able to place it where you need it.