That is one of the annoyances of booking two tickets.
Your best option right now would be to call airtran and see what they can do, or maybe find someone in atlanta who can take care of this for you
I know what can you do it was a special with air France only from boston.
The end of the story (I hope) is that they are not leaving tonight from atl till 10:30 and after spending an hour on the phone with AirTran I was able to accomplish more than my mother running around the airport in atl as she kept on switching from air France to air tran and they are able to send the luggage back to atl and she will get it tonight 2 hours before her flight.
I hope everything goes smoothly.
Oh they also refunded my points and gave me $100 vouchers - חצי נחמה