Each window represents a restriction to the air flow. The greater the pressure difference across the aperture, the greater the flow.
An electrical analogy: each window is a resistor. The current through the resistor is proportional to the voltage across it - but when you have two resistors in series they must carry the same current (air that enters through one window must exit through the other). If the total voltage across the two resistors is constant (the "force of the wind"), then if one resistor is smaller (the "big window") it leaves more of the voltage available across the second resistor (the "small window") - thus the over all air flow will be greater. See this diagram:
So yes - it makes sense to open the larger window fully. The pressure drop across it will be smaller, the pressure drop across the small window will be larger, and there will be more air flow through the apartment.