I guess it depends on when you bought your tickets whether it makes a difference when you pay it, online or at the counter. Here are the details from AirTran's website:
Second Checked Bag
For all reservations booked on or after August 14, 2008, the charge for a second checked bag is $25. For reservations booked before this date, see the table below for applicable fees.
Second Bag Fee, as determined by reservation booking date:
Booked on August 14, 2008, or later - $25
Booked April 22 August 13, 2008 - $10 online, $20 at airport
Booked on April 21, 2008, or earlier - Free
When I traveled with AirTran in September when checking in online I seem to remember a spot where it asks you how many bags you have. And I think you could have paid for the second bag fee there. Of course, paying for it there you would to use a CC. I am sure you can use cash if at the counter. I did it with US Airways a couple of weeks ago.
When coming back and if you are using RAC you will need a CC. They don't take cash. Otherwise, you will have to take all of your bags with you and checkin at the airport.