I haven't done the cruise package in a couple of years, but when I went, if you got picked up at the resort, it was 11:00 am. They will give you an information packet when you sign in at the Cruise line desk in the Customs House.
They had an option where you could reserve to go to one particular park or Disney Quest and they would pick you up there at 12:00 pm. The first year was DHS; the second year was Disney Quest, and the last year was AK.
If you opted to go to the park or Disney Quest, they had reps from the cruise line - i.e. at AK, it was right at the building in the front - where they tagged your day bags and let you keep them there all morning until it was time to catch the bus to the port.