Hi David,
I have a special needs son and have found that Disney is a great place for Guests with Special Needs. When you arrive at the first theme park of your visit, stop by Guest Relations and request a Guest Assistance Card (GAC). Describe your son's needs and they can tailor the GAC to best meet his needs.
Fantasmic! is an awesome show but it can be a little intense for smaller children. At the age of 2, some kids have a hard time understanding what is make believe and what is reality. Some parts of the show can be a little scary (i.e., when the giant dragon appears). The music can also be very loud which frightens some smaller kids. There are also some pyrotechnics involved in the show. My DS5 now loves the show but when he was 2, it was wasn't his favorite. You know your boys better than anyone but I've heard of instances when small children have become frightened.
You could prepare them by telling them about the show - keep your description upbeat and fun. You may want to watch some videos of the performance prior to your trip. You can find lots of them on YouTube.
I'd suggest speaking with a Cast Member when you arrive at the Ampitheatre to ask about alternate entrances or your son staying in a quiet location while you wait in line. Be sure to show them the GAC and explain how he could best be assisted.
When you arrive at the top of the Ampitheatre, look for a Cast Member holding a red flashing light and ask about special seating for your son. There is wheelchair seating along the top row and companion seating in the row just in the front of it. If you feel that he or your younger son may become frightened, you could ask to be seated on the end of a row in case you have to make a quick exit.
Wishing you many magical memories :-) Allison