When you book the excursions online you will choose the time you want to leave. The water park doesn't typically open at Atlantis until 10:00. I'm pretty sure the times we did the Aquaventure thru the ship we met at like 9:00 or 9:30 because we seem to get there just after things are opening. The website will tell you a time to leave of like 2:30 or something in the afternoon. Don't worry about that. Pay attention to the all-aboard time then give yourself an hour or so to get back. The transfer buses for the ship will run continually in 20 minute intervals all day. I don't get exactly why they do the return time online. I've never paid attention to it.
Our first cruise we sailed we did first seating dinner because of hubby's indigestion. We *hated* feeling rushed to get ready for dinner. It felt like it cut into our afternoon. All our cruises since we've done 2nd seating and hubby doubled-up his meds for the indigestion. It's worked out well for us that way.