You list the letters in AMCAS and designate which letters you want sent to which school.
Lets say you send in letters A, B, C, D, and E.
You can send A, C, and E to School 1.
You can send A, C, and D to School 2.
You can send B to School 3.
You designate what you want sent and where. Just make sure that the letters are going to make it to AMCAS before you assign them to schools because you can't "unassign" letters, I believe. I know you definitely can't remove them. I had an advisor that never sent in a letter and I still get a letter from AMCAS stating they have not received the letter. Luckily, I didn't assign it to any schools.