You should be able to figure it out, you just have to keep after it.
I successfully used Chief Architect Pro to design my house and I am a stupid policeman with zero experience/training in design/planning/engineering...
The stairs are affected by the ceiling height. Is your problem with the stairs that they won't reach all of the way to the second floor? The default is 8 feet for the ground floor ceiling height, IIRC, so if you are using 9' or 10' ceilings on the ground floor, then your stairs won't reach all of the way up to the second floor. You have to go back to the beginning and enter the correct ceiling height in order to get stairs to "go all of the way up."
Our ground floor ceiling height is 10' and the second floor ceiling height is 9'. However, the truss design gave us another 2', making the living room and dining room ceiling height 21'. Adding to my problem (in Chief Architect Pro) was that the stairs go up to a bridge that is a 27' unsupported span across the living room.
You just have to keep at it, and you will eventually figure it out.
As for the roof, are you trying to use a parapet roof in your design? I don't believe that Chief Architect Pro has that capability, or at least it didn't in 2007 when I used the software. I had to make a third floor and then make the "walls" on that floor only 3' high. I can't remember how I figured that out, but somehow I did...
Keep in mind that you are going to need a Structural Engineer anyway, so he will "clean up" any loose ends that may arise.
Good luck on your project.