Complex shed roof - almost there but need some help

[HopeToReno]

I'm evaluating Home designer Suite 2014 for a reno. Awesome so far! Currently I'm trying to model the as-built and having trouble with the complex shed roof. See House photo and elevation attached.

Article 492 on clerestory roofs was very helpful, (http://www.homedesignersoftware.com/...?faqNumber=492), however I'm left with two challenges:

1) When I built the roof, an additional attic level was added. See external3d attached. How do I prevent this?
Note that in my case the rooms have no ceiling (vaulted) and I set the finished ceiling (F) to 155", but got something much higher.
2) Article 492 fails to explain how to move the 'temporary' walls back to the original design. (How do you get to the picture in step 5 from the picture in step 4?)

As you may have noticed, I have the additional challenge over 492 of TWO clerestory walls, and a shed wall perpendicular to those. Is this causing trouble?

Any guidance would be much appreciated!

Jack