Trying to get my Airtran Elite status transferred to my SWA Rapid Rewards account: I called SWA Rapid Rewards Customer Service, and after 10 minutes on hold, they are not sure how to do it. After that, I called the Airtran Elite desk. She took both the Airtran and SWA accounts for my both my wife and me. She said the gal who did it was on break and to wait 30 minutes.
So, echoing another reply, this is definitely easier if you call Airtran.