Hi, Anna! Thanks for bringing this great question to the Disney Parks Moms Panel! Having just booked a reservation with a Fairy Godmother-in-Training for my girls, I can definitely help you link it to your 
My Disney Experience account! 
 First, it is important to note that this type of reservation differs to your
 Disney Dining reservations as they can only be added as a “note” on your My Disney Experience account and not actually linked as a reservation. To do so, log in or create a My Disney Experience account, then select “add a note” on your daily itinerary. This way, you will be able to see your
 Bibbidi Bobbidi Boutique reservation on your daily itinerary and the 
My Disney Experience mobile app! If you are having technical issues in doing so, you can
 contact Website Support who can further help you. 
 I hope this helps with your planning and that you have a magical Walt Disney World Resort vacation! 
 Jen