I'm trying to work with my ex on our custody agreement about out Autistic son, but he doesn't believe me abd wont work with me.

Many parents struggle with the idea that their child might have a disability.  Fortunately, it sounds like you have accepted it and are trying to get your son the services he needs.  You know that the more services he has early on, the better his chances are later in life. While you cannot change your ex to make him see the benefits of therapy and structure, you may be able to show it in a custody proceeding.  Of course it would be better if you and his father were on the same page, but maybe you can work out a custody schedule that does not affect nap time or therapies.  If he is exhibiting behaviors when his father does not follow through, you can explain that to the court.  The first thing I would recommend is that you document your son's behaviors on a day-to-day basis, particularly if he has target behaviors in the wrap-around program.  Note the good and the bad, every day of the week.  This will help the wrap around team and therapists devise a good program for him, and it will be easier to explain any changes in behavior to changes in routine.  The therapists may be able to help you provide documentation in a way that is useful to them.  That same documentation and the recommendations of the professionals, can be presented in a custody action if you need the court to intervene to help your child.  Find an attorney in your area who understands both custody law and special education law because that person will be best able to guide you through both issues.  Good luck.