I can't imagine the courtyard will be indoors, so id have to imagine its one of those 2 openings in the building. It makes too much sense especially since the Courtyard is already rumored for part of the queue.
One thing I've wondered and maybe its been asked, but is any of the interactivity going to be on the first level? As in, the stuff on the left next to Mario kart, entrances are on the 2nd level and Toad's Cafe is below it, but is there any room below Peach's Castle and part of the Yoshi ride for more interactive play or just on the top left?