At Boyd's Group Internation meeting recently Gary Kelly of SWA, said that technology to allow SWA-FL to link up flight schedules is due in 2013. Meaning you can start on either SWA or FL and make connection at some point to fly the other airline. Also on the fee front, Kelly stated they have not decided how to merger the fees of the two carriers:
http://www.dallasnews.com/business/airline-industry/20120917-southwest-airlines-airtran-to-link-up-their-route-networks.ece
http://www.dallasnews.com/business/airline-industry/20120917-southwest-airlines-airtran-to-link-up-their-route-networks.ece