This guide, designed to help families developing an Individualized Education Program for their special needs student is published by Autism Speaks Family Services and it seems to be very clear and helpful.
Advocates for Children has numerous programs and resources to help families and students.
Carol Greenburg at NY Special Needs Consulting is a Parent Advocate who helps families navigate the process of getting appropriate services for your child. She is the parent of a special needs child as well as an adult with Aspergers Syndrome, so she has been there and understands it all from the inside out.
If you have experience with any of the IEP process and have found helpful resources, please let me know so that I can list them here as well as in the Resources page of the website.
This article, Tips for Changing Schools, from the Child Mind Institute might be helpful when starting a new school program.