Everyone has their own way they like to organize their thoughts and ideas. My son does everything on the computer, my daughter and I love spiral notebooks, some people use notecards. Here are a few ideas that might help you find your organizational path.
1) Do you like to write or type? As I mentioned, I love spirals. They litter my work area. So to find anything I label the outside of the spiral with titles such as "characters" and "notes" or "places". I try to keep my main thoughts and characters toward the front and the lesser thoughts to the back, but after awhile, they just blend together.
2) So the spirals get a little out of hand and I have to move to writing everything on the computer and have folders I can organize with just a move of the mouse. This is more ideal for some people. My son spends hours organizing his files, so I'm assuming there are others who like to do the same thing. For me, it's more of an end process. I take my spirals and their creative notes and organize them once I get them out of my head.
3) Notecards. Some people like to put a thought or character on note card and organize them in a way that makes sense to them. It is a little more time consuming because then you have to physically organize the cards, but if it works for you while you write, then go for it.
What ever method you choose I recommend some major points to write down/keep track of:
1) Characters and where they come into the story. Also why they are vital, relationships to your main characters, and any secrets you have associated with them.
2) Places. You want the places your characters go to be consistent. By giving yourself notes, you will ensure they will be.
3) Notes! This is probably the most important part. There is a small section in my story with a side character that I hint at something grand.... and I can't remember what I meant by that "hint". I pound my head a lot about it and hope I find a note or something amongst all my papers so I can figure it out. Hopefully this never happens to you!
Happy Writing!