Though I am no doctor (studying computer engineering, with a biomedical engineering option), I have to say that the brain is very fascinating
the brain is a complicated thing and you are right, it is hard to differentiate between the realm of philosophy and of psychiatry (if there even is a distinction). This is why depression is such a weird thing. Some peoples brains seem naturally inclined to darker thoughts, from a neurological, rather than a philosophical standpoint. it is natural to feel crappy and depressed if you are experiencing stress of some kind, however I also know that some people are naturally more content or discontent than others.
as for "telling the difference" I think that if you truly believed in dark things, it would be something that you would admit to all the time regardless of how you feel. Whereas the latter is the opposite, coming only at times you feel the worst.
I suppose that is my two cents, I am not sure if I answered your question. I think talking with someone close about this or a counselor would help more than random forum discussion, as talking things out always helps me. Best wishes!