Everyone doing any Blue Lagoon excursion (Beach Day, Stingray or Dolphin) all take the same ferry to the island. Once you get there people go off to do whatever they planned.
There are then 2 Ferries that go back to the ship. One at 2:00/2:30 and one at 4:00. You can go back on whichever you prefer.
When we went in Feb. we got to the Island, went directly to Stingray City, swam with the stingrays. Then we explored the island a bit, went to lunch (included with all 3 Disney excursions) and then swam a little at the family beach. We wanted to visit the straw market so we took the 2:00/2:30 (can't remember) Ferry back to Nassau.
Here's another possibility I wish I had thought of. On the way back the ferry stopped at Paradise Island right near the Atlantis resort. (Don't know if it always does this) If I had known it was going to do this we would have got off there and checked out the resort, everyone says it is spectacular,and then taken a cab back to the ship.