E.B.
Are you flying out of the country or staying within the US? Does your daughter have any form of ID issued by your state? You can contact whomever provides services for her (Medicaid, or her doctors) to inquire what kind of IDs are available and how to obtain them.
Have one of her doctors write a brief statement about your daughter. Include a description of her disability, and a statement about what she can and cannot do. I had my daughter's doctor write that she is unable to walk long distances, and had him list her diagnoses. If she requires medications or special food or liquids, list those too. Make several copies of the letter and have it handy at each point in your trip.
Get a list of medications from the pharmacy. Make sure it's on the pharmacy's letterhead, and includes the name and phone number. This will be handy in case you run out of or lose her medications while traveling. Again, make copies. Find out in advance if your pharmacy has a branch in the city where you'll be going.
If you're bringing meds, have them in a separate ziplock bag in their original containers with her name on them.
If she needs certain vitamins or over-the-counter meds, have those in a separate ziplock bag with the doctor's letter stating that although these are not prescription, they are required for her condition.
If she needs foods or drinks, have those in a separate ziplock bag with the doctor's statement saying that these are required. I brought Ensure and juices on board the plane because I handed TSA the bag with the bottles and the doctor's letter stating that my daughter required extra nutrition at all times. The TSA guy did carefully examine the bottles but there wasn't any problem.
www.tsa.gov has a separate section on traveling with people with disabilities.
Hope this helps some!