With Southwest it is pretty much a cattle call for boarding. You are assigned to a group A, B or C. A's are parents with children under ten and the disabled. A's are boarded first. After they find seats, B's are boarded, after they find seats C's are boarded. The first to check in and print boarding passes are assigned the B's. You are allowed to check in online at 12:01 am the day of your flight.
We flew Southwest once to Florida and we were B's and my DH, DS (12 at the time) and I did not sit together because there were so many people with children under 10 that boarded before us.
We have flown Air Tran the last two times and really like them. You can check in online the day before your flight and on the day of your flight you can upgrade to business class for $35. a person if available. We have done this both times and it's great.