A few comments - while there will be different document styles around, I'm sure, and differences in different States,
(a) looking at the GAMA style manuals, which appear now to be fairly ubiquitous, the AFM generally is embedded within, and is part of, the POH.
The regulatory required bits (ie the AFM pages) will be identified in a suitable manner, eg there might be a margin highlight that "This page is FAA-approved" or somesuch. These are the bits which are tied up with the certification and must be observed.
The non-regulatory bits comprise the remainder of the POH and represent OEM recommended practice and the like. Good gen but not with the force of the regulatory process.
(b) Flight manual supplements are part of the flight manual and are applicable when the relevant modification is embodied in the particular S/N aircraft to which the POH applies. The supplement, in effect, replaces the appropriate bits in the basic flight manual .. it must be read and applied. Anytime you jump into an unfamiliar aircraft, it is essential that you read the whole POH/AFM, including supplements to establish just which are relevant to the aircraft in question.
Typically, for civil flight manuals, there will be all sorts of supplements included - only those relevant to the particular airframe build apply .. the remainder can be ignored.