Sarbjeet,
During initial training (until line training) you will get an Alien Registration Card. This allows you to remain in Japan for longer than a passport visa. Once the training is finished you will hand back your card and enter/leave Japan on either a Shore Pass or, if you want to fill your passport up with stickers, you can use your passport. Most people will use a Shore Pass during their time at work and maybe use their passport on their last trip, before going home, to add some flexibility to their travel arrangements......especially if they are using ZED tickets.
Regarding your PM. I cannot reply by PM as you are too new and don't have a mailbox. BUT, my reply would be to sit down with several cups of coffee/tea and read this thread. All your questions have been asked and answered several times.