I don't know if the Hyatt lobby check-in is just for those who stayed in the Hyatt or not, but that's where they tell you to go when you stay there. If you book your air through the cruise line and choose the "Night Before" option, they'll put you up there as part of the package. I would imagine that it doesn't matter where you meet the bus. They can check your name off the manifest regardles of where you check in.
I would say that your best bet is to book the transfers in advance, if that's how you plan on getting to the port. There's really no reason not to (i.e. it won't save you any money). If you have booked the transfers, your docs should tell you where to meet the bus.