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This isn't really an answer, but there are research papers that used DesignBuilder to assess solar chimneys here and here. They both used the CFD module in DesignBuilder to analyze the air flow within the solar chimney and adjacent zones.

In DesignBuilder, the solar chimney area should be an "Unoccupied" activity since it is an empty space where no occupants, lighting, or other internal gains are located.

Other than creating a "Hole" between the solar chimney and adjacent zone(s) that allows airflow between them for CFD simulations in DesignBuilder, I'm not sure about the CFD boundary specifics to set in DesignBuilder.

Having 2 inlets and 1 outlet would be OK if you have 2 zones adjacent to the solar chimney, each with a hole to allow airflow to enter the solar chimney. You should have only 1 outlet for air leaving the solar chimney at the top.