[I have realized that the question is for the opposite direction: London-JFK-ATL. This answer is not wrong, but doesn't apply to this question. I am leaving it for now, as it might still be useful]
No, but yes.
Generally, you don't need to leave the secure area to check in for a further flight, as airlines have a transfer counter inside the secure areas, and you could also go right to the departure gate and get checked in there (at min 30 minutes before the flight, though!).
However, as you are arriving from an international flight, you will need to go through immigration and customs, and after that, you will be outside the secure area. This is intentional, as the flight you arrived was potentially not checked according to the US security standards (there are flights arriving from many airports anywhere in the world). As a consequence, you will need to re-enter through the local TSA security, so you could as well check-in right outside at the counters.
Even if your flight is immigration pre-checked at the departure airport, you would probably arrive in another terminal (as the domestic flights don't go out the international terminal), so you would still be forced to walk outside security to change terminals.
You should try to check in for your onwards flight while you are at the counter in London, the agent should be able to clear you in the system as he/she sees your passport and visa at that time.