You will have to check in on Sunday morning before you go. Your Ultimate Park Hopper (UPH) passes will be encoded onto your resort ID. You can get the ID even if your room isn't ready yet. Once you get the new resort ID, head to the parks.
Bell services will hold your luggage until you return later in the day and your room is ready. Are you staying at the same resort for both reservations? If so, make sure the front desk knows that you have continuing reservations and you probably won't even have to pack up your luggage. They will most likely (but not guaranteed) allow you to remian in the same room.