We did the same routine last year, and it was quite painless.
We used "Dive with Martin". They have a small kiosk right there at the cruise terminal, just as you pass the guarded re-entry area (for cruise ship passangers only). You tell them you're there to dive and they will give you directions to the dive shop, which is also located at the cruise pier. You walk over to the dive shop, check in, pay for the dives, and they walk you to one of their boats that is harbored right there.
Nice and easy...........
We had a split boat with a total of 4 experienced divers that stayed with one DM on the tours, and there was another 4 new divers that went with the other 2 DM's. Our bottom times were not compromised by the other group as we headed in different directions and just got back to the dive boat a lot later. Very good dives, and good DM's.
One suggestion would be to go to their website and look around.
www.divewithmartin.com If they seem like you will use them, then send them an email inquiring about diving and pricing on your selected dates. Tell them you'll just meet them at their cruise ship pier location and an approximate time. You can get a much better rate than the "walk up / cruise ship diver". We dove for about 50% less than anyone just walking into the dive shop, or being escorted by the kiosk sales person. Just tell them you have a reservation.
Good luck, and enjoy your cruise.