I would call to see if it will be necessary to check in twice, my guess is yes.
Whenever that may be, this is where you will check in and your room key is also your KTTW card for the cruise. You do not turn your docs in here, they will take them on the bus to the port. Then, you basically get off the bus, go through security, up the steps and that's it!!!!
When we did it, once up the steps after security, we walked right through the terminal through the Mickey ears and onto the ship. At this time (1pm) there was no line to get on the ship. If you are not too much in a hurry, take a look around the terminal is pretty cool.