There are a bazillion ways to organize the "facts" of the world you've created. I would recommend computerizing your information rather than notebooks (although if that's the way you create best, by all means start there), simply because you'll need to search out a term or make sure you don't contradict yourself eventually.
You might divide up your facts into people/beings (whichever inhabit your fantasy world), with details about individuals from appearance to behavior to social standing; other living things (monsters, magical beings, etc.); places, with as much detail as needed ranging from big-picture (the fantasy world's planet) to region/area to cities, towns, villages, or farms, to specifics of a single inn, cottage, or brewery, and last, individual rooms in which scenes take place; and things, items which do not exist in this world but are common there, and have names and your descriptions of what they look like and how each is used.
There are many other fully workable systems, but that one may suit you.
Maryn, hoping this helps
