It depends upon *how* you're checking the car seat and stroller. I would agree with the PP - you won't *need* the car seat until you get to Orlando. In my experience, it was easiest to check my kids' car seats when I checked in and checked my bags - if you ask the Delta agent nicely, they
may even have a large, clear, sealable plastic bag that they can put the car seat in.

Make sure that you see them put a bag tag on it and get your "receipt" from them in case it gets lost.
That said, when my children were in the 6 month to 2 year old age range, I oftentimes brought the car seat on board to put them. My DS was not a good flyer - it was easier to strap him in and give him things to do. Granted, you don't have as much room, and you lose easy access to the tray table and front seat pocket. Additionally, you'll need to carry it through Atlanta (ATL) until you get on the next plane - we ended up using the stroller for that, and carrying our child(ren). That's a personal decision.
As far as a stroller goes, I've always gate checked mine. You need to do this as soon as you get to the gate (or as soon as a gate agent is at the desk) - don't wait until they start boarding (just makes more of a hassle for everyone involved). They will put a tag, usually pink, on your stroller.
IF YOU WANT THE STROLLER IN ATL, tell your home airport gate agent so that they can mark the tag appropriately. The ramp agents will bring the stroller up for you to the jetway so that you will have it when you literally walk off the plane.
You will then need to get another gate check at the next gate for your next flight. IF YOU'RE NOT CHANGING PLANES, you can essentially gate check the stroller all the way through to Orlando. Again, when you get to Orlando, it will be in the jetway waiting for you. Double check with the gate agent that's doing the tag at your home airport to confirm where it's been gate checked through to - Atlanta (ATL), or Orlando (MCO).
When my kids were small, it was always good to have the stroller readily available to walk through the airport, especially ATL. A 2 hour layover will go fairly quickly - between getting off the plane, determining where your next departure gate is (do I have to change concourses or walk pretty far to the next gate), walking to that next gate, taking a potty break, getting food (depending upon the time of day you're flying), etc. Some concourses/areas of ATL also have a small play area for the kids (think: Little Tikes small climber).
Good luck on your trip! And enjoy your time at Disney!
Lynne