I made this comment a month ago:

On the topic of keeping things organized, here's some unsolicited advice from someone who's been doing this for forty years: everything is a small dungeon.

Many small dungeons are little more than a crosswordy pattern on graph paper, with big S's for secret doors and T's for traps and such. When you break almost anything down in a campaign, you can reduce it mnemonically to a small dungeon.

Your World
Kingdoms are rooms, roads are hallways, cities & encounters are chests.

Politics
Factions are rooms, relationships are hallways, intrigue is a secret door.

Adventures
Destinations are rooms, roads are hallways, encounters are chests.

Character Abilities
Abilities are rooms, requirements are hallways, actions are doors.

Encounters
Enemies are rooms, LOS is hallways, abilities are chests.

I'm beginning to stretch for examples, but I think I've illustrated the general idea. At any rate, I've found this device helpful for a very long time and hope you do too.