There have been many questions about how to model basements whether they are conditioned and unconditioned.  

For unconditioned basements - REM will calculate the temperature of the basement depending on the basement wall constructions and locations as well as the location.  As a result, foundation walls, slab, and frame floor separating the conditioned space and unconditioned basement must be defined.  The thermal boundary can be defined at the frame floor or the foundation wall or let REM decide based on insulation levels in each surface.  

Conditioned basements - REM assumes the temperature remains at the setpoints and foundation walls and slab be included as inputs.  A frame floor is not required as this will be an adiabatic surface since the thermal boundary is at the foundation wall.  

The decision to model a home with a conditioned basement or unconditioned basement depends on the location of the HVAC equipment, the ducts, the registers, the insulation location and what temperature the basement is resting at.  There is not always one clear answer - so some engineering judgement is required in those in between cases.