Yes you can use your credits toward your fees. Now if I explain the whole thiing, I would be writing a short story.
The short version is call Airtran and ask what their procedure is for using credits to pay for your luggage. They will tell you to go so far online and then call their number when you get to a certain point in the online process. They will finish the process from there. It would be better to call them to get the exact details and at what point to call them.
What we did however was a little different. First thing is that we paid the $6 a person advance seating fee so we can sit together and not have to take a chance on picking seats for free at the 24 hour mark when you check in. By the way you can use your credits to pay for the advance seats too. Just call them when you want to pick your seats.
Now when we were at the 24 hour mark to check in, a screen came up and asked me to upgrade to business class for about $60 each. The fee depends on how far your flight is but dont quote me on this. My flight was PHL to MCO. Longer flights might cost more. My luck is that my flights dropped so much from the time I bought them that I had enough credit to almost cover the upgrade cost.
If you get that upgrade option, stop checking in online and call in for help to take advantage of the upgrade if you want. Make sure you get credit for your seat fees from before because there is no charge for them in businees class. Also bags are free in BC so make sure that is not charged as well. If you have enough to cover the BC upgrade it is a nice deal since you dont have to pay for bags.
The key to this is to call in to use your credit in whatever way you want to use it. You cannot use the credit online at all!! Again you must call in there is no other option.
Good luck!
