The queen excluder is to keep the queen from laying eggs in the supers. Normally honey is only taken from the supers allowing the bees to keep any honey and pollen they have deposited in the hive bodies. If brood is allowed to be raised in the supers, you would have a much more difficult time trying to reap nice clean honey. It would make it pretty much impossible to sell honey without first filtering it.
In my case, she will have two deep hive bodies in which to lay her eggs.
When bought bees are first introduced to a hive, the queen comes in a cage because number one, the bees that she is shipped with are not the bees that raised her and already are devoted to her. She needs to be protected while the rest of the workers become acclimated to her. The cage entry is currently filled with a mini marshmallow that the workers will slowly remove by eating it. By the time the marshmallow is gone, the workers will know her as their queen and will not attack her.
In a few days when the weather has warmed back up, I will check the queen cage to see if the queen has been released. If she has been released, I remove the empty queen cage.