Assuming the gbxml import preserves Spaces (e.g. surfaces, loads), in the OpenStudio Application (as suggested here):

• first, add new zones in the "Thermal Zones" tab
• (optional) edit them beforehand, e.g. rename, add thermostat schedules, sizing parameters
• switch over to the "Spaces" tab (just above)
• link (drag-and-drop) newly created thermal zones to the right spaces

This can be automated with an SDK-based script if the model holds hundreds of spaces. Hoping I understood your question correctly.