We fly Airtran a lot, and we always have strollers/carseats. You can push stroller to gate and check it when you board the plane. There's usually people waiting at the end of the jetway where you get on the plane or they'll be a cart there, or, just fold your stroller up and leave it there. Ask for help if you're not sure where to put it. They'll put it in the plane, and it'll be waiting for you on the jetway when you get at your next stop, whether it be layover or destination. Gate checking assist devices (such as stroller) is free.
I almost always check my carseat/s. You can do that where you drop off your other checked luggage. It flies free.
I have a bag for our strollers and carseats just to keep them cleaner. I used to not do this, but then my infant seat got beat up, so now we bag them. Your little person does not need to use the carseat. Airlines/FAA say they are safer in a child restraint seat, and if you ask about it on the boards, get your popcorn out because it's usually a big debate. Do what you think is best. I check mine.
Hope this helps!