This is an image of my ~\Library\Mobile Documents folder on my desktop:
Why are my files under com.mentalfaculty.ensembles.clouddata rather than BookstoreInventoryManager (which is my app name?) Is something set wrong in my app?
You'll note that there are two BookstoreInventorManager directories. The top one is the mobile documents for your app. You can see that the ensembles folder is inside that one.
I suspect you are creating the other one yourself. There is no harm to this.