I'll echo what others have said - a commute on an RJ is much more difficult than mainline. Even though you'd be less senior in ATL, hotels are a lot cheaper and mainline planes cancel less in my opinion, and are rarely weight restricted. When I commuted to NYC as a new hire, I would almost always take the mainline plane to LGA and cab it to JFK than gamble on getting on the CRJ-200 going to JFK.
As a note, the reason someone suggested picking an airplane that is based in NYC and ATL is that you can switch bases whenever your seniority allows you. Since you wouldn't need any training. That would be the 717, 737, 320 and 7ER that are based in both locations. (well and A330 and 767-400 but those aren't a new hire plane... yet...) If you need training to go to a different plane, you would have to wait for your new hire seat lock to expire (1 or 2 years, not sure)