I sent this question to my friend Fred Bostrom who has run 25 straight Bostons (which puts him into a special club). This is what he wrote:
Alan,
Every marathon that I run in is certified. A couple days after I run the marathon I get an E-mail that says that all of the results have been sent to the BAA. I have no idea how the BAA then sorts out and keeps track of all of the qualified runners but apparently they do it very effectively.
Fred