The easiest way is to call Airtran. You can call after midnight on the day before the flight (2 days if you are Elite), this will give you a jump on people upgrading when they check in.
Upgrading to Business Class: ... All members may purchase an upgrade or redeem four A+ Rewards credits for a one-way upgrade anytime beginning the day prior to departure.
Getting Business Class Upgrades: Call us at 1-888-3-A-PLUS-8 (1-888-327-5878) to reserve your upgrade to Business Class anytime beginning midnight the day prior to departure. Four A+ Rewards credits are required to redeem for a one-way Business Class upgrade. If an A+ Rewards member wishes to upgrade a companion as well, an additional four A+ Rewards credits will be required to redeem for a one-way Business Class upgrade for the companion. Availability of Business Class seats on AirTran Airways flights is subject to capacity controls and blackout dates, and seats are limited and may not be available on all flights.
If you are using Airtran Credits make sure you have the account number(s) of the account(s) you will be pulling Credits from.
If you are transferring points from Southwest, transfer them before you call.