I just figured this out for myself a couple of weeks ago... so easy..
After you have created your roof, use the "vertical opening" tool to cut the section of the roof that you dont want .

First go to the "Architecture tab and find the "vertical opening" tool as shown in the photo above.
After clicking the tool, click on the roof that is creating the problem.
Now use the project browser to get to a view where you know the roof is causing the problem. Most likely, a plan view.
Here's the catch... you wont neccessarily be able to see the problem roof as you go to sketch the void. You have to know where to place the "void sketch" based on where you know the roof is protruding.

When you're done sketching, click the big green check mark, and the void you created will take the place of the roof that you were dealing with.
Love this tool...
"It's not the size of the dog in the fight, its the size of the fight in the dog....."
George Hobel
Reflections of Charlotte
Residential Building and Design