"Long Axis of Building" fields on Airflow Network: Simulation Control

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If I understand your question correctly, you have set "Wind Pressure Coefficient Type" to SurfaceAverageCalculation and you are asking about the "Azimuth Angle of Long Axis of Building" and "Ratio of Building Width Along Short Axis to Width Along Long Axis" fields. Assuming that is correct, yes, you should input 90 and the ratio. Here's the picture that's in the docs:

The calculation that is done here is not directly influenced by the geometry rules as far as I know. The code computes a wind pressure curve for each of the four cardinal direction (N, E, S, W) and then associates the surfaces (which have had geometry rules applied) to these directions. The closer that your building is to being a square, the less the angle and ratio will matter. I have also seen these left as the defaults, even with non-rectangular buildings, which isn't super great, but is probably an OK approximation in the absence of better data (e.g. computed from CFD).