Every author organizes their writing a little bit differently. Some can only work on a completely clean desk and use sharp pencils and separate every chapter into a different file. Others curl up with a pen and a spiral-bound notebook and scribble away with cats sleeping on their feet. Some write down daily word counts or chart out their time spent. Others just go with the flow and finish the book whenever it's finished. Some set goals, and others are more flexible. What kind are you?
I'll tell you what kind I am ... I'm all of the above. And you might be too.
There are several different factors that play into how I organize. The first factor is the nature of the project itself. Some projects need a lot of planning, like a historical fiction novel. You need to know when all the battles took place and just when George Washington gave that impassioned speech so you can work it in properly. You need to research the clothes and the food and the social rituals of the time. But other projects, like a contemporary comedy, might be best written in a more laid-back way.
Another factor, at least for me, is my life and what's going on in it at the time. If I'm super busy, I tend to track things out more because I know that I'll have limited time to work and I want to be productive. I'll jot down notes of upcoming scenes so I don't forget them, and then I'll set time limits or goals to try to reach my self-imposed deadlines.
There really is no right or wrong way to write. You can be as messy or as organized as you want, or any combination of the above. You might have a notebook for each work in progress where you write down every thought that came to you while you were in the process--whatever works for you. That's the ticket right there--finding out what works for you, and for that project. And if you discover that New York Times Bestelling Author Amazing Dude's system doesn't work for you, don't beat yourself up over it. That's his system, and you can find yours.