middle floor with multiplier at midpoint elevation
gap
ground floor at ground elevation
any below grade structure
also be certain to set ceiling and floor of middle zone to adiabatic, or use the otherside coefficients model and set that as the boundary condition for the floor and ceiling. Also, you can set the middle floor boundary surface to the middle ceiling boundary surface and vice versa, but you will get some warnings.
the really important part is to make sure that the middle floor ceiling and floor boundary conditions are not sun and wind exposed.
the reason that I put the typical floor being multiplied at the average elevation is because energyplus actually calculates the air property variations with elevation.