Read the last comment and thought I'd offer some solidarity... and my own brand of organizing
I've been inputting Golarion-related background and the rabbit hole is so deep, my Places section and the People section were
out of control. I settled on a structure for places I think will make things a little easier to navigate (for me. Smelly players... never looking at my precious)
Top level
Planet
-Continents and Oceans
--National Entities and Major structures (glaciers, mountain ranges etc...)
---4 stubs per nation:
---
Major and minor settlements (Capital on down, based on Gazetteer)
---
Interior Features (sub areas of natural spaces like forests, rivers, mountains that were created from whole cloth at the previous level)
---
Major NPCs of (insert nation/area here)
---
National Groups (like the National Army, or spy groups, government)
----Each settlement gets 4 containers (used or not)
----
Local Groups (local adventurer's guild, Loyal order of Waterbuffalo, that kind of thing)
----
Local NPCs of Note (the cast list of people not likely to affect the nation, but matter to the town)
----
Major and Minor Districts (no settlement is homogeneous)
----
Adventure Areas (catch all, local swamps inhabited by rabid chickens, what have you)
The pattern for settlements can be applied to
Interior Features if it is inhabited, like a forest full of druids.
For example:
Golarion (planet)
-Avistan (continent)
--Taldor (National entity)
---King Jerkface (Nation level NPC - he can travel so pinning him to the capital doesn't make sense)
---The Jerkface Knights (National Group)
---The forest of Ugly Sticks (interior feature)
---Cassomir (city)
----Abbey Green (District)
----The local Hangman (Local NPC - he's not going anywhere short of a war)
-----The Pub in Abbey Green that the local Hangman drinks at (location in a district)
This way when I open up RW, I just collapse the Hierarchy and then open to the specific place I may want without a lot of little stubs open everywhere.
And since I repeat this structure multiple times, I do go through the
Names dialogue (Ctrl-Shift-A) and set the linking to "never" for the container topics.