We've flown AirTran quite a bit and I always prefer to sit as close to Business class as I can in the coach section. I've never noticed the alternating loading mentioned by the PP, although maybe they do it that way on some flights. If you don't pay for priority boarding it is business class first and then back of the plane forward from my experience. And, yes, that has meant at times we have had trouble finding a place for our bags. Our last flight back from Orlando, one of our bags ended up several rows behind us. It wasn't a big problem for us as we were in no hurry to deplane, but if you are, it might be worth paying for priority seating.
ETA: I did have an epiphany on this flight that I might be better off to choose a few more rows back as it seemed the flight attendants were storing their bags in the first coach overhead bin thus limiting available space in that one.