I am looking at flights from CHS to EIS. Looks like I can book all the way through with Delta. My layover in SJU is 48 minutes. Seaborne is SJU to EIS. Is that enough time?

It's enough time if your inbound flight is "on-time" and you are doing only carry-on. Problem is, if your flight from CHS is delayed, you'll miss your connection.

I'd opt for a longer connection time (90 minutes, at the least). Remember, there's no real downside to waiting in the airport for your connecting flight but if you your inbound flight is delayed and you arrive at your connecting gate 1 minute after the plane leaves you've missed your flight. Murphy's Law of Airports is always lurking around - Error on the side of a longer connection.

..but of course your other problem is that, if you're doing only carry on, on the SJU to EIS leg, you will most likely have to gate check the carry on bag. Just make sure there is NOTHING in there for those kind baggage handlers in SJU to steal. I recently had to gate check a perfectly legal carry on bag in SJU because the overheads were full. I had packed a small carry on that I knew would fit under the seat, with my camera, lens, and jewelry, inside the carry on bag, so I took that out to make sure there was nothing they would want.

But overall, I would be with Fletch on this one. It probably will be ok, but I HATE tight connections on vacation, as I stew about it for months before hand.. If it's one ticket, they would have to still get you there, but it also kind of depends on what your options are if you miss that connection.

What about on my return to San Juan. How much time should I need to leave for connecting flight to Atlanta?

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

Speaking of SJU...Does anyone know what tine the Duty Free opens up on a Saturday morning?