If you're still interested in this, then here's a synopsis:
The seniority list was calculated to mix AirTran pilots into the Southwest pilot list. Some complicated formula, that no one can accurately describe, basically took an AirTran pilot's original date of hire, then essentially subtracted so much time, and plugged him into the Southwest list. The AVERAGE loss to an AirTran pilot was 2-1/2 years (but individual pilots lost anywhere from exactly two years to just over three years-I don't know how it was decided). So if the average AirTran pilot was hired there in, say, Jan 2001, then he would have plugged into the Southwest list next to a Southwest Jul 2003 hire. That's the new Southwest seniority list with everyone's name on it.
The big caveat with the second deal (the one that got ratified), is that no former AirTran pilot can be a Southwest captain before January of 2015, and all of them are supposed to be transitioned by then. (Also, they make AirTran ALPA CBA wages and benefits while on that side of the partition, and get SWAPA CBA wages and benefits when on this side.)
Come Jan 1, 2015, there's no fences whatsoever. Any Southwest pilot, whether orig Southwest or former AirTran, can bid any seat and any base that his global seniority can hold. It is expected that all the upgrades from that point for a while will go to former AirTran pilots who were senior enough on the list to be a captain, but were contractually forbidden to do so until that date.
All that make sense? Hope this helps answer your question.
Bubba