If your school has some sort of rec letter file where they collect your letters and then send them out, you would most likely use that. Then when all your letters are in you would ask them to send the letters to AMCAS. Or you can use programs like Interfolio or have the rec letter writers send the letter straight to AMCAS if it's being written during your application cycle(aka don't send letter to AMCAS 2 year before you plant to apply)
Then when you fill out AMCAS you'll say "send my letters to these schools" via the primary application program.