Normally, when you buy a codeshare ticket, you would go to the counter of the airline OPERATING the flight.
For example, an American Airlines flight on an American Airlines aircraft departing from an American Airlines gate could also be a codeshare flight for a half dozen other airlines, each with with its own flight number for the same flight. However, the passenger would go to the American Airlines ticket counter -- even if, for example, the passenger bought it as a British Airways flight.
In the case of AirTran and Southwest, parent company Southwest has been consolidating the ticket counters and gates of the two brands, as it works toward the complete elimination of AirTran by the end of 2014. By now, Southwest and AirTran ticket counters should side-by-side at every airport that still has both brands (although there might be an exception somewhere).