Organization is something I've slowly progressed from loathing to loving as I've grown older. Up until fairly recently in life I did, and could, almost literally keep all the relevant details for games I was running in my head. I could do the same for work. As time went on, and the amount of stuff I wanted to keep in my head increased, that kind of broke down. This has led to the very real problem of having to learn how to take notes, track notes, and organize those notes along with NPCs, locations, maps, pictures, and all that on top of things.
In a lot of ways this has been as frustrating as when I realized part way through majoring in Japanese in College that I had no studying skills because up until then, I had simply never needed to study. I don't say this as a brag, but as a pointer that I am very much in the early stages of my 'getting organized' journey, and that that is ok. Life throws a lot at all of us. You juggle it as long as you can, but then you need somewhere to keep things because you can't juggle all the things all the time.
Also, if you've been holding back, I've also found this: I'm happier the better I get at keeping things organized. This is true in my games as well as in my life. My mind is more free to handle things because I don't need to keep 80 things in mind all the time. They have a place to go, and I can grab them when I need them.
That said, let's talk about organization and your game.
Make/Use The System That Works For You
As a disclaimer, and also a piece of good advice, what works for me may not work for you. What works for you may not work for me. Like with all advice, take it, chew on it, figure out if it is right for you. If it is, take it and make it yours. If it is not, see if you can learn anything from it and then discard it.
Accessibility Not Storage
The first thing I've learned is that there are two ways to organize or store things. The first way is when you are packing things away. Everything goes in its place, and you pack it as efficiently and neatly as it can be. The second was introduced to me as 'combat loading' where the idea is you organize things so that you have quick access to the things you need fastest.
When it comes to running a game, accessibility of information is key. When your players decide to do a 180 and head back somewhere instead of progress forward. Or decide that the next step in their plan to travel to a Dwarven City some 100 miles away is to travel 1000 miles in the opposite direction, you want to be ready to pivot and handle that.
Accessibility also comes up in your planning. When you're looking for an antagonist to bring back, an NPC to return, or a plot line you want to reference being able to find it is important.
Use As Few Containers As Possible
The second thing I've learned is that while very detailed granularity can be very nice to look at it is also a lot of work, and it doesn't stop being a lot of work. You want things organized. You want things organized so you can find them. You also want things organized such that it is easy for you to sort and organize new things as they are developed.
Remember, a game is a living thing. You're going to make new NPCs. You're going to make new locations. You're going to make new maps. Those will all need to be sorted and filed after each session in order for you to be able to reference them again in the future. The easier that sorting is for you, the more likely you are to keep up with it. It is a lot less work to dump a new NPC in a folder named 'NPCs' than it is to drill down into NPCs -> Continent -> Kingdom -> Region -> City -> District -> Neighborhood -> <Race> -> NPC. Finding the sweet spot between those two methods that works for you not only in finding what you need quickly and efficiently, but so you will keep up with your organization efforts is going to be something only you can figure out for yourself.
Maintenance Is Key
Putting everything in a bucket is great. But if you just leave it in the bucket, it loses all meaning and just becomes a bucket of stuff until you pull it out and go "Hey, I remember this!" The same is true if you just accumulate a pile of stuff without ever sorting it into the correct buckets.
Remember, we want this system so we can access the info we need when we need it. That means maintaining the system so the info we need is where we go to look for it when we need it. This can be as easy as just making sure you sort your notes after a session and add relevant details to the appropriate lists. Or it can be as complex as going through the system every now and then, reviewing what you have, and figuring out what is still needed, what can be discarded, and what should be brought back soon lest it fall away forever.
Plan It Out Before You Do It
Finally, and this is where I am right now, plan out your method before you do it. Take some time to jot down ideas for your organization buckets. What will let you access what you need when you need it? What do you need right at your finger tips? What can be deeper in the drawer? Do you use a cloud system, your local computer, or something completely non-digital? Perhaps a bit of both?
Planning it out and testing it will save you from putting in a huge investment of time and energy for something you then decide you hate. Give your brain time to chew and digest. The idea is to save time down the road, not begin a never ending cycle of planning and overhauls.