Complex zone in Honeybee

Hi Ladybug+Honeybee team,

Firstly I would like to thank to everybody in this community for all the passion and time you put in this group. I've learned many things from your discussion, your example files.

I have done a lot of things with Ladybug and Butterfly tool in my project for daylighting and wind simulation.

Now I'm starting with Honeybee tool to run energy simulation. And I stuck at the first step. I went through all topic that I found in this group to solve my issue. Unfortunally, I still don't understand how can I define the zone in my project.

I made a simple model to explain my  issue as you can see in the attached file.

Greyzone: Big living room with lots of windows around.

Blue zone: Storage room which is a half underground.

Green zone: Kitchen which is inside and same level floor with the greyzone, 

Red zone: Bedroom which is a half outside and a half inside. It has the glass windows to look out side and inside

Pink zone: Working room (half inside and half outside). It's directly connected with the inside space and glass window outside

Yellow zone: Skyline.

They are connected to each other by stair case. 

 As I see in many example file, Zones are at the same floor and they are not intersect each other. My situation is opposite.

Could you help me clarify how can I define the zone in this situation to have the correct energy model?

Thank you for your time,

lam,