Hello! You can take the reservation number you got and go either online or call Air Tran and pay the additional fee to choose your seats ahead of time. I highly recommend this with flying with a toddler! We flew last year on Air Tran from Midway and it was WONDERFUL! We used to fly out of O'Hare and now feel spoiled with Midway:
1. It was much easier to get to for us;
2. NOT CROWDED (we flew out on Thanksgiving Day). We ended up having enough time to watch some airplanes (for the 2 year old) and get a nice breakfast in. The year before we ran to our flight.)
3. Check-in: walked right up to the attendant - no line;
4. Security line: fast, efficient, prompt.
Anyway, as for the toddler I would like to suggest a game. When we are driving we play the airplane/school bus game. A point for every school bus you find and 3 points for every airplane. This not only kept her occupied in the car, but got her excited to get on an airplane. I would ask her where the airplane was going and she would always say DISNEY! I have NEVER flown with a toddler so easily (2 previous hellish trips before with older two. DH still over anxious about flying - I tell him not to panic the toddler and to be an adult and get over it).
Good luck and remember even if your toddler gets upset, spills or is a little too loud - the majority of those people on the plane have been there, done that! Enjoy!