By definition different fluid regions must be separated from each other by solid regions. So you will not be able to setup two different concentrations that are not completely closed off from each other.
Flow Simulation cannot solve mixing problems (of two different fluids).
But you may be able to create the conditions you are looking for by using two different initial conditions (initial conditions for the air in the pit and initial conditions for the air above). Make a solid of the air in the pit, turn the solid off in component control. Then use that solid to specify a different initial condition than the general initial condition.
If your goal is to try to find natural recirculation I would turn off the transient mode. Try to find a steady state solution before looking at a transient model. Then when the steady state model is behaving as you expect try looking at time stepping. Flow Simulation solves every problem transiently, attempting to find a steady state solution.
That worked - thanks!
I'll take a look at the steady-state problem first, then turn on time-dependent analysis.