Our Operating Handbook (how the plane gets flown, checklists etc) is approved. The FAA (well, the POI that signed off on it) is in concurrence that this is how he would do things if he was in charge. Or Flight Ops Manual (how the airline operates things such as security procedures, crew checkins, uniforms etc) is accepted by the FAA that they are ok with how we do things.
I don't think they can take enforcement action against a breach of something in the accepted manuals (although the company can certainly discipline for it) where as they can enforce violations of approved materials violations.