I try not to book tickets like that in airports I am not familiar with to prevent needing to reclear security. Since all of ATL is connected behind security I have connected from FL to DL and v.v.

IIRC...Airtran would let me check in online (for their flight) whether I was going DL-FL or FL-DL, but DL would only let me check in if they were the first leg

so:
DL-FL check in for both online
FL-DL check in for FL online, but in person for DL.