Before starting to write a fiction story, you always need to have an idea that could make such a good story, in your opinion. Then you need to work on that idea, to develop it. You can write a first synopsis then take more or less notes on paper about your plot and characters, you can also do all of it mentally but anyway you always have to plan your future work.
Personally I quit taking notes, I just think a whole lot about what I'm going to write before actually starting to work on paper or computer. I mean I quit taking notes some time ago, when I started writing screenplays, which is an easier (or less difficult) thing to do than writing books. Fiction writing is a hard job, it can take much time - especially when you write a book, which is incredibly difficult - so I'd rather do it naturally, use my instinct. And new ideas come to you while you're writing. I remember a line in the movie Finding Forrester, from writer Mike Rich and director Gus Van Sant, starring Sean Connery: "You must write your first draft with your heart. You rewrite it with your head. The first key to writing is... to write, not to think!" I won't say that this is what I do most of the time but it's the best definition about the way I do it: instinctively. I put on paper or computer every good idea that gets through my mind, trying never to lose my vision and style.
So the first thing I do when I get a good idea is think about it a lot, and build it (beginning, middle, ending, etc.), no matter how I do it, if possible without taking notes at all, BEFORE starting to turn that idea and concept into a book or script or play or whatever. Then as soon as I start writing I don't think no more - or if I do, I don't do it too long or too intensively, it could lead me to writer's block. I just follow my instinct and let the story lead me to where it's supposed to end. And I try never to put any heavy psychological stuff in my texts, I always try to define my characters with what they say and do, as much as possible. This way my works can be read quite easily and quickly, and the reader will never get lost.
I'm always surprised when I manage to finish something. And I'm even more surprised when I manage to get promotion for it. Actually my last notable work, Charlie's Trips, is also the first of my works to get a publicity campaign. Two good reasons to be pleasantly surprised about that one. All my previous works have been left unpromoted - and I've been writing stuff since the mid 90s.