Hi Sherril!
Thank you for bringing your question to the Disney Parks Moms Panel. I actually had this same question myself when traveling with my infant so I'm glad you asked!
You will want to
make the reservation for the number of seats that you'll need at the table. So when I travel with my husband, myself and my little one, I make the reservation for 3 so that we have a spot at the table for his high chair, even though he usually just eats off our plates. I made the mistake of making it for 2 once and the table we were initially seated at had difficulty accommodating the high chair. The Cast Member quickly brought us to another table, but I learned that day!
I also wanted to let you know that the Chefs at Walt Disney World are fantastic at assisting
Guests with allergies! I would recommend putting the note into your Advanced Dining Reservation. If you forget to do this, when you are seated just let the Cast Member know that someone in your party has an allergy and you'd like to speak to the Chef. They will come out to your table and let you know at each restaurant what is okay for your nephew to eat and what they would recommend. They can often make something not on the menu too to help accommodate his allergy so he can enjoy a meal with the rest of the family. It is totally up to your sister and your nephew what they are comfortable with, but I think you'll find that Walt Disney World is well versed in handling Guest allergies!
Please let us know if you have any other questions before your trip!
-Lindsey ºOº