As stated, your target is to organize information. And that is usually not a trivial task : information elements are linked to others, may be linked to space and/or time. So you can have different axis : you can for example use a geographical map to locate things in space, a timeline to organize them in time, some family tree coupling time and relationships between siblings, etc.
Depending of the level you want to achieve, it can be quite a lot of information to keep in your head. You may want to use some tools to organize this. It can be simple notebooks and papers, or some software (I can think of the great Tiddlywiki here ; feel free to add suggestion in comments).
If you are building this for a world or game, do not push it too much, as the world is mostly a recipient for your story, and not an end by itself. Structure your information around the hero or center of the story.
As a side note, you can maybe find inspiration for both content and organization in some gaming systems like Microscope.