AirTran Airways A+ Rewards - Another Upgrade Question

If I my intinerary is JAX-ATL-SFO, can I just upgrade the ATL-SFO leg during online check-in?

What happens to my luggage fees?

If not online, can I do this with a CSR at the 800#?

Tnx

You can upgrade ATL-SFO only but you will still pay bag fees.

thank you