thank you everyone for clearing this up for me! Gate checking the chair seems like it would solve some of my dilemma. I guess he would still have to use the folding type chair from the gate to his seat as he is not able to walk at all. I plan to take him to the restroom right before we board, so hopefully the size of the restroom on the flight shouldn't be a problem!
Oh good. I was having heart palpitations from your initial post. Under NO CIRCUMSTANCES would I willingly hand over my powerchair to baggage check. It is effectively my legs and the only one I have. If it gets broken (as powerchairs sometimes do), I am pretty much housebound until it's fixed.
I believe under the current laws governing disabled air passengers, no US airline can force a person to surrender their powerchair prior to the gate. I was forced to give up mine at Heathrow last August flying British Airlines, but I chalk that up to the lousier European disability laws (currently improving) and some very beligerent baggage handlers (they went on strike the week after I left). You should have seen how many parts they delivered it to me after my return to the US.
Contact AirTran before your flight about your powerchair and aisle chair needs. (User cannot walk, needs aisle chair, must gate check powerchair, powerchair batteries sealed gel cell/airline safe, weighs such-and-such with and without batteries, etc.). Just keep repeating the mantra as you go through the various check-ins. When you get to the point of surrendering your chair (usually around the time you board the plane), take as much of the chair onboard with you. Anything that is easily removable and breakable. Usually that includes seat cushions, footrests, sometimes even armrests. Make sure your chair's batteries are disconnected and ask to speak personally with the baggage handlers taking your chair to the baggage hold. That way you can explain how to disengage the motor locks for freewheeling, engage them for parking, reassure them about what type of batteries you have (most every powerchair these days uses sealed gel cell batteries, the only ones approved for air travel), and any other concerns you may have about the chair's weak points.
You'll probably be the first folks boarded on the plane and the last folks to get off, but the chair should return to you at the gate you arrive. If not, (because the gate is for some reason innaccessible for the baggage hold), then you'll get a personal escort (with manual chair and pusher) to a special holding area where the staff reunites you with the chair at the airport.
You may also want to snap a few digital pics of your chair before you give it up. That's just in case any damage is caused and you need to file for claims. Most airlines are getting very good about handling powerchairs these days, but you never know.
Oh and, know your rights but be especially nice in how you present yourself. Any staff will more likely be helpful to pleasant flyers than crabby ones.
One last thing for fture powerchair travelers, wherevever possible opt for a DIRECT flight for all your travels. The problem with is that connections your chair is then being unloaded by a set of baggage handlers you haven't spoken to and may only know your chair by the luggage tags. That has sometimes led to chairs being not loaded onto the connecting flight. If you must take a connecting flight or surrender your chair to those not taking it to the hold directly, you can ask the flight attendants to check the chair was loaded onto the plane before it takes off. When I flew home from London I did just that. Where Heathrow's handlers aggravated me, BA's flight attendants reassured me. My chair did return with me overseas.
- you'ld think that's it. 
You can gate check one wheelchair. They don't look at the weight of it, but at the number of wheelchair(s).
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