It's super overwhelming. I plan trips for a living (
travel agent) and plan my family trips all over the world, but planning our upcoming Japan and Hong Kong trip has been a challenge. A fun challenge, but a challenge!
The best way that I have found to get the cheapest airfare and hotel is twofold: One, search a package on Expedia to include round-trip flights and your Tokyo hotel only (you can pick to just have your hotel for part of your stay). Second, search the largest cities within driving distance as your airport. Also, you can use Kayak to search a range of dates to see which days will be the cheapest to fly on and use those for your Expedia search. I was able to get my family a very good deal for this summer using this method. We are then staying in Hilton Tokyo Bay for our TDR portion of our trip.
Another way to save money is to look into AirBnbs or VRBO rentals. These are not only cheaper than hotels, but you can cook, which saves a ton of money. You can also open up a hotel reward card that is having a big sign-up bonus. We prefer IHG, so I am also getting free rooms in Hong Kong and Hiroshima and Narita. In Hong Kong it's the Intercontinental Hong Kong!
The only way my family is able to travel as much as we do is because I am a budget traveler!
Lastly, reading these boards has helped me a ton to create an itinerary for the parks. The Facebook page is also a good place to ask questions.