When you make your PS for the full service restaurants, ask the CM to note his allergies. The CM will also give you the phone # for each restaurant for which you have a PS. You need to call the restaurant at least 7 days prior to your PS. You can speak with someone at that time to let them know his specific needs. Then, when you arrive at the restaurant, ask to speak to the chef before placing your order.
I also have the phone #'s for the food and beverage managers in each of the parks. You can call them to ask about ingredients in counter service places as well as the food carts. I don't have the #'s handy right now, but if you need them, PM me and I can find them for you.
Disney is wonderful when it comes to food allergies. We are heading to WDW this May and it will be our second trip with our DD who is allergic to peanuts and tree nuts. On our last trip, we were very comfortable with every restaurant we went to. We seldom eat out at home, so it was a real treat to eat out every day.
Good luck and have fun!