My first thought it to suggest that you combine your interest in seeing Atlantis with your desire to interact with dolphins. Both pursuits, I highly recommend!
One of the greatest adventures that I have ever experienced was swimming with dolphins. Yet, the Atlantis Resort is absolutely beautiful and a tour of The Dig (aquarium) would be well worth your time.
Atlantis, on Paradise Island, offers more than a full day of fun. While the Blue Lagoon dolphin excursion is highly rated, it would be much more relaxing to spend your day in one place.
The Blue Lagoon Dolphin Encounter lasts approximately 5 hours with departure times at 9:30 a.m. and 12:45 p.m. The Discover Atlantis Tour is approximately 2-4 hours departing at 11:15 a.m. and 1:15 p.m. Note that times are subject to change.
Combining the two tours would be impossible given the above timeframes. It may be possible to go on your own to Atlantis in the morning, however I would be concerned with getting back to the ship in time for your Blue Lagoon tour.
Personally I would select one destination and soak up the magic of that location.