Dave,
it depends on the operation of the two fans.
If both units runs simultaneously, then you would treat that as one system but with two fans. With that you would add the Supply Air, Return Air and the Outside/Ventilation Air as if they are coming or served by one unit.
If the fans/units cycles, then you need to define that control strategy and why they would cycle and what each unit would serve when it runs by itself.
I lean toward option one! because the building would be considered as ONE air system.