Thanks everyone for the replies. I realize the way SketchUp recognizes solids means that adding these walls precludes the volume from being recognized in the SketchUp world as solid volumes, but had hoped there was some workaround here.
What I have done is as suggested, modeled 2 separate solid volumes. I'll be talking to the guy doing the energy calculations today. He uses several different programs, as well so maybe there is an answer from his side.
I'm also thinking that just because SketchUp see's things this way, doesn't necessarily mean his software will, if I use a single skin separating partition wall with openings indicated.
Thanks again, and I'll let you know how this works out.