I played dumb and emailed Air Tran to ask where I could enter my Known Traveler number in their system now that Southwest has agreed to participate and they are, after all, one big, happy family now.
This is the generic cut-and-paste response I received:
Unfortunately, at this time, AirTran Airways does not participate in the TSA Pre-Check Trusted Traveler/Global Entry program. I would recommend checking www.tsa.gov periodically to see if their program has been expanded to include AirTran Airways. I do apologize for any inconvenience this may have caused.