The merger between SW and Airtran isn't going to change anything (from what I heard). They are going to keep different names and the only addition is that SW will be going into airports that Airtran goes into now. For me that would be a bonus because Airtran goes out of my local airport, but I find it cheaper to drive to BWI to get a flight to Orlando.
You have heard wrong! AirTran will cease to exist, and only Southwest planes will be flying - probably some time in 2012.
http://www.southwest.com/html/about-southwest/lowfaresfarther.html?int=HOMEAIRTRAN00000110502