As others have said, you will need to book your Tokyo Disney trip portion yourself. The first thing you need to notice with their booking website, is that it is down between 3am and 5am, Japan time. If you're on the east coast, that means that between 2pm and 4 pm during daylight saving time, you can't consult anything when it comes to prices and package availability.
How many people are traveling? Many rooms are for 2 people or 3 people max, such as the Chip n Dale character room I stayed in at the Ambassador Hotel last year. There were two single beds and what I figured was a pull open sofa bed at the end of the room.
You can book rooms for 1 to 5 nights on your own. Depending on the hotel you book, starting the day after you check in, you have access to the Magic 15 entrance at one or two theme parks. 15 minutes before everyone else, a special set of turnstiles opens, allowing hotel guests with the proper document to enter the park without waiting in the massive lines before opening. This sounds like nothing, but japanese guests are very punctual and will start lining up at 6am for an 8 or 9am official opening. They are also very savvy regarding Premier Access or Priority Pass (free fast pass equivalent), so they will already have started to scoop up the good rides.
If you're willing to prebook a large portion of your trip at a price premium, you can do a vacation package. Those are for 1 or 2 nights max and depending on the one you book, you need to select your dates and length of stay. It will then ask you for what style of package you want and then you select an hotel based on availability. You then book premium access to rides, restaurants, etc. and then you get the price of the package. You also get a drink voucher, which another poster did a list of places where you can use it on another forum thread.
Food is very different compared to the american parks. For example, you want a burger? Only one or two venues per park will serve them. Substituting or removal ingredients from the dishes is culturally not a thing in Japan and you will need to use their Special Dietary Menu if you have allergies or intolerances to food.
