I just dealt with a similar situation....had been working around similar situations for a while, but I figured out the answer while I was looking at this posts.
First I set up my smaller gable roof so that it extended well into the main roof and so it completly intersects the main roof. Then I join the roofs using the Join Geometry tool (NOT the Join/Unjoin Roofs too)- this will show the valley line in the roof plan. Go to your roof plan and edit the smaller gable roof that lays on top of the primary roof. Edit the footprint so that the footprint follows the valley lines. That worked for me.