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This depends *heavily* on how you are running the game.

For a sandbox I just had each location in its own folder on my computer, with a map or the original adventure I used for that location there, and then a text file with notes and changes, and another for random encounters.

Cities had a rumour table, too.

Folders on a computer have a natural hierarchy, which makes this fairly reasonable approach.

While in case of Apocalypse world you would organize your game in terms of fronts, and in case of Sorcerer you would have the diagrams and those would be renewed when new kickers would be created, creating an episodic structure where only that stuff which is in focus in this story is considered in detail.

There is no general solution. You may want to specify what kind of game you are running and how you are structuring it (sandbox, railroad/flowchart, relationship map, etc.) and then we can help more.