In the wizard, when you define the building footprint and thermal zones,
there is a box directly below the zoning pattern called "Zone
Characteristics." If you go to that screen, you can select a zone and make
it multi-level conditioned (or unconditioned). If you select multilevel
conditioned, you can specify conditioned height and some loads for the lower
part of the space. It may assume that it connects all the levels in that
shell, and I'm not sure how it would behave if you wanted to have the atrium
span through multiple shells. In that case you may have to use a shell just
for that section as has already been suggested. For a simpler, one shell
building in which the atrium goes all the way to the top, however, I think
you should be able to make the wizard function work for you.

Hope that helps,

Doug