The precise sequence is not that important. LORs should be collected and assembled by your undergrad or postbacc premed advisor/committee office, and not sent directly by you or the recommender to the schools. Once you have completed your AMCAS (primary) application, the schools you indicate will be informed that you are planning to apply, and will set up the appropriate files. Your undergrad/postbacc can send out the letters any time after that, which may be before your secondaries are complete. (In my experience though, it sometimes takes longer to chase down LOR writers and get them to complete than it does to finish up the secondaries.) Anyone else please correct me if I have misstated anything.
