Jo_Ann

corrections made
 

On floor level 0, draw half walls. Set their thickness and material like concrete walls.
Add the stairs.
 
On floor 1Create your terrain perimeter, (shown as hatched region).

On floor 1, turn on floor reference, and place a terrain hole,  shaped to your "room". (shown as blue)

On floor 1, draw an elevation region (shown as orange).

 
 
Elevations shown are just guesses.
You keep leaving the forum, making it difficult to help.
 
 
  

When you have the stairs correct  (no rail on the right side, closed stringer) then place it where it belongs.

The easiest way to add the curved shelf, is with a slab.  Size it the correct height and thickness to rise above the stair stringer, then arc it's shape around the stairs.
Finish it off with a custom countertop , curved around the slab, for the surface.

Curved slabs and curved countertops aren't as finicky as curved walls.
 

Adjust the thickness of the flared backsplash, then copy/paste it away from the walls.
Select, and butt it up against the side wall of the garage extension.

What I see, when looking at your jpeg image, is that you've used glass shower walls to draw the shower as an entirely separate room within the bathroom.  This makes it an 'island' room, and auto drawing a connected divider wall to an existing wall, is how the software deals with this type of room.

corbels
 

1) I do not see that large fir wall designated as a "railing".  Draw a railing wall over it, and change it's style in the railing wall dbx, to show only posts to ceiling.
2) On floor 1, delete the wall directly below the balcony railing wall, and the balcony railing will show correctly.
3) The balcony needs to be shortened, and the stairs extended over to it, to avoid bumping into the exterior/roof wall.  You can then set the portion of the new wall at the top of the stairs, as "invisible".
4) On floor 2, uncheck "flat ceiling over this room".  Architectural does not build rafters, so you will have to build your own (use sloped soffits).
 

So, do the same thing that you did up front.
The reason it didn't work for you in your video, is because you have to keep a small gap between the dormer wall, and the interior wall.
 
  

The front wall of the balcony can not extend beyond the 1st floor wall beneath it, if you want the roof to continue in front of it.

What Eric said is important, so I am just guessing....
But maybe this will get you headed in the right direction. 

The 1st pic is the original cottage.  Pics 2&3 are the vertical flip of the cottage.

My floor plan might help you with your settings.  Pay close attention to the garage/house NON connection on level1.
Delete your 2nd floor and rebuild using blank plan with finished ceiling height as shown  (or do a 'save as', then delete the 2nd floor).   Align walls as shown.
Pay attention to ALL floor/ceiling settings, roof pitches, and walls.

The roof between the front breakfast room and garage is a problem area with auto roofs.  You could add a sloped soffit to make it look better.

When the roof is correct, turn off auto build roof, and rejoin the walls between the garage and house.  Invisible walls will probably be needed to maintain some floor/ceiling heights in that area.  Go slowly.

Redraw the interior walls on the 2nd floor and raise the ceiling heights within the usable rooms.

Because I had to trace the floor plan (to work on it in HDA10) the dimensions are not exact, but they are close. It may not be perfect, but I hope this helps.  
 
 



WeebleSue cottage flip.plan

Use a base cabinet set as a peninsula base.   In 3d window, drag the bottom of the cabinet all the way up to the bottom of the countertop.  Open the cabinet dbx/front tab.  Select and delete the toe kick.  Only the countertop should now remain.
Use a soffit for the narrow rectangle extension.

If you open every one of the wall sections on level 0, and uncheck 'foundation wall', the floor reappears.
 
Like Kbird said, there is a rogue wall section south of the ship (on level 0).
 
I also noticed that there is a gap between floors 0 & 1, at the front (south) side of the ship.

Ross,
Tools>display settings>display options>rooms,interior area (put a check).
 
In your reference manual, look at rooms>room labels for an explanation of the different room labels.

After you have turned off 'auto build roof', the program will then allow the use of the material painter to paint individual roof planes.

Use a half-wall  (railing wall)  instead of a foundation wall.
Make this wall the thickness and texture of a foundation wall.
Open the room spec of this 'room'  to alter it's elevation.
Open each wall spec to change it's height.

There is a wealth of information (with pictures) in the knowledge base.
 
http://www.homedesignersoftware.com/support/article/KB-01197/52/Home-Designer/Roofs/Creating-a-Prow-Roof.html