I suggest this workflow

1. Create the geometry exactly the way you are doing it now

2. Use the Extension > OpenStudio User Scripts > Alter or Add Model Elements > Assign Building Stories feature in the SketchUp plugin to assign stories.

3. Write a Measure to assign space names. Something like:

   model.getBuildingStorys.each do |story| story.spaces.sort.each_with_index do |space, i| space.setName("#{story.name} space #{i}") end end

4. Use the Alter or Add Model Elements > Add New Thermal Zone for Spaces with no Thermal Zone feature in the SketchUp plugin to create a zone for each space.

5. Use the Alter or Add Model Elements > Add New Thermal Zone for Spaces with no Thermal Zone feature in the SketchUp plugin to create a zone for each space.

6. Use the surface matching feature, then click Intersect in Entire Model to cut surfaces that don't overlap perfectly into smaller surfaces.

7. Use the surface matching feature, then click Match in Entire Model to match the newly subdivided surfaces up.