You are asking quite broad questions here.
Sounds like you need to start with a travel agent to describe some options.
Then buy a guide book to see where and when you would like to go, and what you want to see and do.
The "best" way to holiday here will depend on the individual.
How long do you want to travel? What time of year?
Why are you interested in Japan?
You are only 19, so you probably won't have a lot of money. That suggests you are going to think of hostels for accommodation. Depending on where you end up going, you may/may not want to buy a JR Rail Pass (if you can afford it).