Yeah, I think LORs are supposed to be sent once you are invited to complete the secondary. Do you have a committee packet? If so, I believe that you simply send that to each school. As for where to send it, some MSTP's say to send them only to the MD committee, others say to send them only to the MSTP committee, and others say to send them to both committees. If you don't have a committee packet, then things will probably get more complicated (e.g., if the MD committee at that school wants all your LORs, but the MSTP only wants academic and research LORs).
Since they do a centralized primary app, why don't schools just do LORs the same way? Wouldn't it be nice if you could send all of your letters to AMCAS, and then schools could just download whatever they wanted from there?