As others have said, it's an imperfect system and different people have different experiences. Others have stated that they did online check-in and went straight to the parks without a hitch. Some...myself included...have had trouble doing that. Back in the fall, we stayed one night at AKL before moving the next day to BW for the length of our stay. Did online check-in, credit card on file...all that jazz. When we left AKL after that first night, we just put everything in the car and headed to AK...we'll check in to BW after AK closes for the day, since we will assuredly have our room number texted to us by then. Well, that did actually happen without a hitch, as I received a text around lunch that day. The problem came earlier, when we attempted to go through the gate at AK and we weren't allowed in. We had to go over to guest services at the park to get everything straightened out.
So...hopefully it will work for you, but don't be surprised if it doesn't.