Book on the Southwest website and you'll get 2 bags per passengers free, no change fee but there is a chance your family will be split. Book on the Airtran site and you'll pay to check bags, will have change fee but will be able to pay for assigned seats.
I'm not sure the chances of being split are as large as we'd think. I'd assume a reasonably large number of customers book via he southwest site in order to avoid paying to check bags.