The most common known education organizations for learning functional medicine.
The IFM is probably considered the "Mothership" organization, with modules heavily focused on the science. When CME is involved, protocols and specific labs/supplement companies are not able to be included in individual presentations. Question and answer sessions (in person and online) are set up to address more specifics. Kresser's ADAPT course is newer, and he does mention protocols and specific labs/supplements.
PDF of descriptions/general costs for each program: FM education programs