How can I route storm water away from my atrium?
Can you tear up the courtyard and put a leach field under it before laying down the floor, thus preserving the through-ground drainage now present?

Can you consider rain-permeable material as flooring? (Some ideas here and here, or  investigate other options.)

Other than those, the only idea I've got is a sump, a pump, and run the pump's output thru basement to outside. 

(Or to drain and sewers if that's legal in your area; it isn't here.)