Thank you both for the suggestions as well as clearing things up for me. Correct me if I'm wrong, but combining the mass from the penthouse down to the roof would result in 0 lateral force at the penthouse level. Thus RAM would not be able to design the braces at that level.
Obviously, the ideal situation in this case would be to allow RAM to design the braces for the penthouse but allow me to distribute the reactions from the penthouse to the frames below manually. Would the best way to accomplish this be to simply run two models (one with the mass from the penthouse lumped into the roof, and a second model that is used just to check the penthouse frames)?