Hi Miccal,
I'd model it as you have done so far, but then place an invisible roof plane to use as an SEO to trim the base of the upper wall away. I'd then use the upper wall as an SEO to trim away the top portion of the lower wall so they then neatly join. You won't see the join line if the materials of the two walls match.
You may find that you have to place the main dormer walls on a layer with a different layer intersection number so they don't try to clean up with the lower walls.
Hope that helps.