There is some misinformation in the above postings. I will try to answer you questions directly. While direct flights are always preferred, your outbound through JFK is OK, unless you have to change terminals you will stay behind security, any checked luggage will be checked through so other than some inconvenience and time lost changing planes it will be OK. Nothing unusual. And I would do it if it saves money.
Returning is a different question. JFK is a very busy airport with a lot of international arrivals and therefore potentially long lines for immigration and customs. You have not indicated when your trip is but it will not make a lot of difference with JFK. As a first time traveler I assume you don't have Global Entry - you should consider if you have time. Goggle it. GE is a preferred travelers program - $100 for five year. You are pre-screened so that you can use the GE line on returning to the US AND, equally if not more important, use the Pre-check lines at TSA. That alone is worth the $20/year if you travel once or twice a year domestically.
This is your sequence on returning -- Immigration first. Immigration is now using a automated kiosks - answer some questions (know your flight number), scans your passport and prints out a slip to take to the immigration officer. Can be long lines for both. With Global Entry you use dedicated kiosks with fewer people since the vast a majority do not have GE and a GE line for the immigration officer.
From immigration - keep following the flow - you claim any checked luggage - and on to customs. You hand your declaration slip to a custom officer - they may or not ask any question - then you immediately redeposit any previous checked luggage. In the pick up area and lines to customs there maybe a dog with a handler sniffing around looking for fruits, vegetables, and probably drugs. So don't bring back any fruit. There is also a dedicated line for GE at customs - far right at JFK. Looks for it. It is not obvious.
After customs and redeposit of checked luggage, you are outside of security so it is on your gate and another pass through TSA security. Again - potential more lines. Unless you have pre-check.
With out GE I would allow at least three and maybe closer to four hours to make your connection. With GE you could probably get it closer to two hours. Regardless of what you do, make sure you know the next flight to ATL should you miss your connection.
If you could avoid coming back through JFK I would do it but if you cannot - there are worse things in life than a couple extra hours at JFK. We arrived in JFK from Germany the day that JFK re-opened after being closed because of the blizzard several years ago. That was an experience.