It is hard to say if there will be a long line for check in, it depends on the time of day you check in, how many CMs are working etc.
We stayed there last May and check in was a breeze, we had 2 rooms and both were ready when we arrived (around 1:00/1:30) we were checked in and on our way to our rooms in about 20 minutes.
In order to get to your room you just have to use the internal bus, to get from the main building to your building. It was very easy.
There is a bus stop there and you can go directly to the parks, just check your carry on luggage, if you have any with luggage services and head to the park of your choice.
We found the bus service to be quite good. We used the internal bus system a few times and this worked very well too.
The resort is spread out, but it is beautiful and we enjoyed walking around the lake to get to the foodcourt each morning. If you do not want to walk, you can just take the internal bus.