Soutwest and AirTran should be fully integrated by the end of 2014 according to an e-mail by the airline.
Domestic AirTran flights can currently be booked through Southwest which is a nice option. Over Thanksgiving we used Rapid Rewards points to fly AirTran to Florida and flew one leg on each airline for the way home. It would be nice to have the option to book international travel to the Caribbean with the Companion Pass. However, I’m guessing it would probably take a boatload of points to do so.
When the airlines become fully integrated, Rapid Rewards will become the loyalty program of the combined airline. According to Southwest: We will continue to share information about the integration as it is available. Thank you for your loyalty, and we look forward to seeing you onboard soon.