I usually use range of motion exercises such as stretching. The stretches I do vary, but I try to stretch their hips, legs, and arms. I also use limited weight training. I have them do bicep curls, overhead raises, wrist and forearm, and hand strengthening exercises (squeezing a handball). I have them use 2-3 pounds and do three sets of 8 of each exercise. I do assist them, but try to make them use their muscles. I can tell when they are trying to use them. My middle son, Aaron has a tilt feature on his wheelchair and he will do crunches while tilted. I really think that has helped his trunk flexibility.
I agree that it is sometimes difficult not to dwell on their disease, but I have also learned to embrace it. It's something that is a part of them and it does make me sad to think of some of the things they are missing out on. But I know that if they see my sadness, they may dwell on it too and I think that would be a bad thing. They are the most positive boys and I don't want to take that away from them.
Please feel free to contact me if you have any other questions about the exercise. I am a firm believer that exercise is good for everyone even if they have a physical limitation.

Welcome to the site. My son is almost 8 and we live in Berkeley.
Nice to meet you.
Rebecca