I would also definitely recommend DisneySea as opposed to Disneyland. Disneyland is Disneyland in Japanese, almost nothing different, while DisneySea is unique. Shinagawa to Disney is doable but not recommended as you will hit rush hour.
From what recall, fastpass is paper, and you get one per a certain number of hours. (basically have one fastpass all the time). I think weekday in sept you won't need a fastpass for most things, but I think you'd want to use it on the journey to the center of the earth if in DisneySea. In Disneyland, maybe the pass to get is Monsters Inc.