If you are buying a separate positioning flight ATL-JFK, understand that you do not have a connection. You have two separate tickets. If you do not check-in/present yourself for boarding in time for you QR flight, that entire ticket (out and return) will auto cancel and you will be left with whatever value the ticket has (probably zero, plus taxes). QR does not have an obligation to reroute you or to accommodate you in any way. You will likely have to buy a new ticket.

Given the unpredictability of things like weather, I would recommend you arrive in JFK the night before. That way you have alternatives in case of delays or cancellations. Otherwise your window to get there in time for your QR departure may be very small.