do you mean applying as a non-trad applicant, or to programs that seem to have disparate MD and PhD programs that form a loose MD/PhD program?
if you meant the later...
If you have a committee letter you just include that with supplemental (ie research-focused) recs. Every school has a different number of supplemental recs they require. In the case where there are two separate programs, I have been sending my pre-med committee letter to the MD office, and then whatever number of research-only letters to the PhD office. Its great fun organizing what goes where at the beginning of the process, but ultimately you just send research oriented PhD recs and a pre-med committee letter to every school albeit to different offices.