@eugene_s
I typically manage zones by program types on layers. Here is an example: Customized bldgProgram & zoneProgram lists - #9 by MingboPeng
After getting geometry organized, I will create customized program types for each of them so that I can be very flexible later when adjusting loads or schedules.
In the brand new version of Honeybee (for Rhino+Grasshopper) that we are working on, this workflow will be officially recommended, and there will be more useful tools to support this workflow.
Hope this is helpful,
Mingbo