Hi pgjam, and welcome to the Boards. You will find so much information here, and there is a forum entitled DISabilities that might be helpful for traveling with your child.
The A, B, C designations are the order in which Southwest boards its planes... kind of a "first come, first serve" in seating, since no seats are assigned. The people who get boarding passes first get A's, then when A's run out, they start handing out B's, etc.
However, it won't matter for you, because they have a special seating area for people traveling with small children or people with special needs. They board that group first of all. When you check in at the desk, sometimes they will give you a different colored boarding pass so you can get on before the A's, or sometimes they will just tell you to go over and be seated in that area.
My DD has Sensory Integration Dysfunction and General Anxiety Disorder. Not huge special needs, but she is very dependent on me to shelter her from things that scare her. After a flight where we had the C passes and had to get a volunteer to switch seats so DD could sit with me, we always try to get to the airport early to avoid the problem. However, if we are late, I just tell the SWA hosts at the gate check-in desk about her disorder and they let us board first, even though she is 10 years old and looks fine.
We LOVE Southwest and would fly it any time we could... it has the safest flying record and the staff members are happy and friendly. IMHO, they are the happiest people in customer service I know, after our beloved Disney Cast Members! Do you know to go to
www.southwestairlines.com and sign up for their e-mail specials? They come to your mailbox faithfully every Tuesday, and there are usually new specials every week.
When are you making the magical trip?

Kim