Yes, you'll need to book the hotel for the night before when you're checking in very late. So say your flight departs on Saturday night but lands at 1am on Sunday, you'll want to book the hotel for Saturday night as well. If your reservation started on Sunday, check-in isn't until the afternoon. Even though Disney will try to let you get into a room as soon as possible if one is available, 1am is still technically considered Saturday night from their perspective. They wouldn't be able to let you check-in for a Sunday reservation that early, since it would be considered an entire day ahead of time at that point. Beyond that, there are simply never any guarantees of early check-in anyway.
With such a late arrival, it is probably also a good idea to call the resort on Saturday before your flight leaves and just let them know that you'll be checking in very late and need the room to be held for your late check-in. You wouldn't want any issues when checking-in that late at night if they thought you were a no-show.
When you're landing that late, I would also suggest thinking about just staying at an airport hotel for the night after you arrive and going to Disney in the morning? Depending on the cost, it may be a bit of a waste of money to be paying for a night you're really barely even using. However, it would have its benefits as well, such as giving you extra meal credits if you do the meal plan and simply getting you on property right away, even though it's very late.