Toilet training is a big problem with brain-damaged children, and your task won't be easy. However, since he is in an early intervention program, you have access to a set of allies whose collaboration should be a big help.
First I would schedule an appointment with the director or lead teacher in his program and get the details of his daily toileting experiences when he is at school. How many diapers a day does he use? Is there any daily regularity? Does he have bowel movements at school or only urination? Have they tried any training? If so, what have they done, and what results have they had?
Then tell her that you want to begin a training regimen at home and suggest that the two of you work together. Make sure you both use the same words and gestures. Talk about the kinds of reward you might use. Make sure there is no punishment on either side, as that will only slow down the process. And, don't expect instant success.
Finally, let me say that I am glad your toddler is developing nicely. Sometimes, after the birth of a disabled child, parents are afraid to try again. I am happy for you that you didn't let your natural anxiety prevent your having this experience.
Our parenting advice is given as suggestions only. We recommend you also consult your healthcare provider, and urge you to contact them immediately if your question is urgent or about a medical condition.