stuck, on my roof!

[yard dog]

I am using Architectural Home Designer 9 to draw our existing side by side split(?) house. I am having difficulty with the roof on one side.

I cannot generate a roof that is just 2 planes meeting at the peak which is how it exists. see pic 1.
Also, at some point a hole in the side of the next level occured which I can't seem to get rid of either.

The roof is over an entry, living room, dining room that have a vaulted ceiling and a kitchen with a standard 8' ceiling.
see pic 2 for floor plan. You may notice I have "pulled off to the side" certain parts of the house as it seemed the only way I could generate a straight roof line over bay windows.

It appears the roof is being generated in three parts. One part over the kitchen, one over the dining area, & one over living/entry.
I have altered floor heights, ceiling heights etc to achieve the roof shown in pic 1 which is close but not exact. I would like exact!!(Auto roof is off.)
I have tried building a room above the dining area, labeled as 'open below', and the results are shown in pics 3 & 4. Although the hole in the wall of the 2nd level disappears!?

I have gone back through others' posts, tried various things but can't seem to move beyond this point...I am stuck on my roof !