how to group space by thermal zone

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Hi I am trying to group different space into thermal zone for modeling, While the mechanical engineer group the space by temperature set point, duct work consideration that mechanical zone doesn't aligned with architectural zone/space. For example, one FCU is serving space1 and half of the space2. and sometimes for perimeter zone we have 15 ft depth rule, while mechanical zoning plan split the perimeter zone and core zone in a different way. How to zone the space in those situation ?