I'm not sure I understood everything of what you were trying to do, but here are some recommendations that might help:
- when you use the knife tool, Blender has the annoying tendency to create double-vertices which won't disappear after the "Select All+Remove doubles" combo (instead, you often have to merge the vertices in question).
- from what I see of your shading problem, and if I understand correctly (assuming you have no double-vertices problem), you can mostly address that sort of issue with additional levels of subsurf
- If your aim was to model the mirror holder, in my opinion and experience it is much more advisable to model the truck body and the mirror holder as separate objects, and not try to merge them. Merging objects is more advisable when you need some kind of unity, be it a geometrical unity (meaning: a seamless junction between to objects, like a weld) or a texture unity. Otherwise, in situations like "Object A resting on Object B", merging the objects is not advisable. I agree the surfaces where they're linked should meet properly, but merging the contact surfaces is not recommended in most cases (and not only because it makes the job unnecessarily harder).