CHS to ATL has been upgraded to all mainline flights. If they allow you to book the connection in ATL I would be comfortable with that time. I think ATL normally uses a 40 minute connection time. If the entire ticket is booked on Delta you can check your bags all the way to EIS.
Coming home the risk goes up on the SJU connection. The flights from EIS can run late. If however you have booked the entire trip on one ticket then Delta owns your problem. There are multiple options to route you home to CHS if you miss the connecting flight in SJU. Your bags again can be checked all the way through.
As mentioned by Carol the airport authority in San Juan allows the baggage handlers to supplement their income with any items from a checked bag they might desire so make sure your valuables stay with you!
G