The way it was done on our B2B on the Inspiration in Long beach a couple of weeks ago was we had to wait in the atrium by the Guest Services desk until all passengers were off the ship, we were then escorted to customs and then told to go out to the VIP Check-in building to get our new S&S cards then had to wait until the VIP boarding for the next cruise. The procedure must vary by which port you are at.
There was a couple of issues which dragged the process on. They did not start calling out Zone Luggage Tags until 1000, and when we did get in the terminal to go to the ship the computers went down so we stood in the termial for about 30 minutes.
Not complaining just saying how they did it in Long Beach.