Your concerns are very valid and it's wonderful that you can be honest and concerned not only for yourself, but for your future husband and his son.
Your relationship counseling through the church will help keep communication open between you and him, but more extensive professional counseling will help you understand exactly what to expect in raising a child with special needs.
The best thing to do would be to talk to the boys' doctor to find out exactly what to expect as he is growing up and also to find a doctor in your area that he would be seeing. Ask about support groups with parents raising children with special needs and talk to them.
They will appreciate your honesty and possibly help you come to a decision.
Not all people can handle going into your situation. Blessed are the people that can, and blessed are those that are honest enough to say that they cannot.