In comparing with the NW/DL merger, remember that there already was code-sharing and an FF alliance between them for quite a while prior to the merger period. AirTran and Southwest definitely are behind by comparison.
Earning FF miles on each other would be a starting point, AirTran had an arrangement with Frontier until last year.
Maybe a couple of SW cities worth linking to ATL during this period would be definitely Nashville and hopefully Newark. Bringing in flights from the SW hubs is more logical from SW's point of view, though the big ones are all AirTran cities. I don't know if cherry picking non-AirTran cities like Louisville or Hartford or upgrading service to Jacksonville would pass muster with regulators during a time both carriers are supposed to act independently.