Correct, when using Kiva for a zone in EnergyPlus, that zone must have one floor surface touching ground for Kiva to calculate heat transfer for. In your case, you can do two things:

1. Keep the zones stacked, but use Kiva for only -2 level zone and change the boundary condition for the walls of the -1 level zone to "Ground" or another option that is not "Foundation" for Kiva

2. Merge the two zones together, deleting the ceiling for the -2 level zone and floor for the -1 level zone or modeling that surface as internal mass instead.zone.

The second option would likely be more accurate, assuming you merge the zones correctly (sum internal gains like lighting, e.g.).