Airtran and Southwest flight question

[Roo'sMom]

Hi
I have a flight booked through Airtran. The first half of the trip is an Airtran flight and I have seat assignments. After the stopover, it is a Southwest flight. My question is- when I check in 24 hours in advance for the Airtran portion of the flight, will that also check me into the Southwest portion of the flight- I'm hoping to get "A" or "B" so we can sit together. I have called both Airtran and Southwest and they just told me to check in 24 hours in advance and to see a gate agent if I have a problem getting seats together. I would rather avoid having that issue if possible. Anyone have any experience with this?
Thanks

 

[Madzac]

This was our situation with our 2013 trip to FL except the first leg was SWA and the second airtran after the layover. We booked through AT so we checked in at AT at exactly 24 hrs in advance and got our boarding numbers (B group) for that initial SW portion of the flight. Going home it was a nonstop AT.

The interesting thing was because one leg was SW we didnt have to pay any baggage fees either way.

 

[Roo'sMom]

Thank you! Interesting about the baggage fees!!