I called AAMC with respect to a similar issue and my impression is that you can not chose what letters go to MD vs. MD/PhD programs at a given school, you designate the letters to go to that school, and they go, with no differentiation as to MD vs MD/PhD program to receive.
My understanding is that for schools that participate in the letter service, AAMC sends a packet to the school with all your letters in it. That's it. Maybe for Duke and the Louisiana schools (not participating in the letter service) you can differentiate programs....but for the letter service schools, most all of them, the school just gets a packet from AAMC (hopefully just once, if all your letters are in before you designate them to schools/get secondaries out).
If I am wrong please correct me! Thanks.