How does Online Shopping work?

Hello!
I'm going to move to Japan next month (April) to study Japanese in Shibuya. The school one is pretty short, so most of the time I have free I will study, but also use any forms of entertainment, of course.

I am a big fan of the Japanese horror series Fatal Frame(USA)/Project Zeru(EU)/Zero(JP) and they just realised their fifth game onto the Japanese Wii U last year. Since I'll be moving there, I don't want to bother buying a European Wii U, besides, playing a game in Japanese will help my studies. Specially with the kanjis.

Anyway, my question is, how does online shopping work in Japan? Where I live (in Sweden) we have to fetch our orders from the post office for bigger packages. They never leave it on your doorsteps. And we also have a internet system called a e-card, were a system randomly picks a card number connected to your reall card, in order to protect your real card information to get stolen etc. So, I wonder if this system is used in Japan too, since I want to buy a Wii U to pass time when I've finished homework a or when I'm not with friends.

Any help is appreciated!

Online shopping delivery in JP is normally delivered by a courier service company such as Kuroneko-Yamato, Sagawa, or JP Post, unless it is delivered by it own self courier service.

You put your full name, address and phone number in JP on the delivery form. The most of online delivery can be requested when(date and time) you want to receive it(eg, 6th March, between 14:00-16:00). The delivery man will bring your parcel on the time you have requested. When he(sometimes She) comes, say "Thank you", then sign on the form to prove that you have receiver it or put an stamp called "Inkan" or "Hanko" which your surname is printed but majority of foreigners don't have their Inkan or Hanko. So you can just sign on that(Clearly).

The delivery man(sometimes lady) comes to your place but you are away, he(sometimes She) leave a note that he(she) came to deliver your parcel but you are away. The note tells which phone number you should call and your ID number on, you call the number and register the ID number, the phone machine asks when you want to receive it, you press the phone digital number then he/she will arrive on the day and time you have requested on the phone. This service is a free of charge.

Alternatively, you can collect your parcel from JP Post branches and/or Kuroneko branches if it's sent by Kuroneko delivery service too while the office is opened.

Japanese courier service is 100% trusted and possibly the best service in the world.

For payment wise you can either pay through Credit Card (some shop may not accept foreign issued card), convenience store, bank transfer, cash on delivery etc.

Those payment method depends on the online shop itself.