Nothing much to say here. I went with 5 letters total. One was from a professor I had in my major, one from a science professor I have a close relationship with, one from a humanities professor I had for over a year, one from my laboratory PI, and finally a letter from a doctor I shadowed for about 100 hours (he is a family friend as well). I wanted some variety for these letters, and although I have never seen any of them, I have heard that they are "strong." My advice is to start making relationships with professors from day one of college. You don't want to ask teachers at the last minute that barely know you. My letters are all from people who know me professionally and personally. To be honest, I don't know how important letters of rec are. Someone can enlighten me, but I can't imagine too much stock being placed in them.
Anyways, each school does it differently, but for my undergrad we simply have the letters sent to our pre-med adviser and she compiles them and submits them through an independent company. This company then adds the letter packet to AMCAS. Fairly simple, sorry for the not so well thought out post, I am swamped at work right now.