That's right. Everyone meets somewhere on the ship (for us, it was the pub) and a cast member takes attendance and gives everyone orange B2B cards. When she gets the all clear, she escorts you to the luggage area and then through security, where someone else picks you up and takes you to testing. Then, when everyone in the B2B group is cleared to board, you're escorted together back into the terminal to go through security and check-in, then you go upstairs and wait in the B2B area right near the bridge to the ship. When it's time to board, you line up and give them your orange card and then go back onto the ship. So, you're just about the last ones off the ship and the first ones back on. They didn't do the welcome song for us the second time, though...
Also, don't forget that there's some free snacks and free coffees (even the fancy ones) at Cove Cafe when you reboard!
EDIT: For Port Canaveral, anyway. I don't know how it goes in other ports. The restaurant manager will come and talk to you at dinner one night and then you'll likely get one or more follow up calls or messages from the officer in charge of handling B2B guests on your cruise. They'll let you know what's up.