It depends on the specialty. Opthalmology for instance has a separate match, so you rank ophtho programs through the SF match and transitional or preliminary year programs through the traditional NRMP. Urology has a separate match as well. Radiology and Anesthesiology both require an internship (note this can be a transitional year, prelim medicine or surgery, among others) and these are all ranked as a separate list but through the NRMP. You don't have to do your internship at the same place as your residency, I am doing mine halfway across the country from where I will be a resident. If you don't match in say, Radiology, you can take a preliminary internship year and then reapply through the NRMP for PGY-2 programs. It sounds confusing at first but once you get to the point that it matters it all really does come together pretty easily.
