The crew leasing companies and ANA will arrange for you to be sent a Certificate of Eligability. You will forward that, along with your passport, to the Japanese Embassy or Consulate for them to issue you a trainee visa. If for some reason this does not happen, you will have to enter the country as a tourist and comply with the time restrictions of whatever your nationality may be. Assuming you are from Antigua (from your profile) you will require a visa either way since there is no visa waiver program between Antigua and Japan.
You will enter the country on your trainee visa until the completion of OJT. After that point, you will enter and depart the county on a crew-member's shore pass.