There are many ways to organize, what I find easiest for me is making folders in my mods folder, My mod folder looks like this,
Build
Buy
CAS
MCCC
Misc Mods
Temp folder
Temp folder CAS
Terrain
I then have subfolders in Build, Buy and CAS as these can be a few levels deep.
Build folder looks like this,
Doors
Fences, Gates, Stairs
Windows
Floors
Walls
Roofs, Foundations
Outdoor plants
My buy folder is pretty much the same, I make a folder for each room, one for decor, indoor plants and one for misc stuff
My CAS subfolders are
Accessories
M clothing
F Clothing
K Clothing (K is for kids as I have both children and toddler clothes in it)
Hair
Eyebrows_Beards_Eyelashes
Makeup_Nails
Shoes
Skins_Tattoos
MC Command Center is in MCCC and my other Mods go into my Misc Mods folder
I use my Temp folders for CC that is newly downloaded so I can check to see that everything is working with it before I move it into its "proper" folder.
Yes, I have loads of CC so I have found this way of organizing CC works for me.
You might wish to also download S4S, it is a big help if you wish to find CC that doesn't have its own thumbnail, delete CC you no longer want, delete color swatches you will never use, I just downloaded a lipstick with 100 color swatches, 50 were color and the other 50 was the same colors only with the mouth gap, which I don't like to use, so I deleted those and the other swatches I won't use, I got the lipstick down to 20 shades that I will actually use in my game, lastly you can use S4S to fix "stuff" that is in the wrong category eg. a party dress that is also in the bathing suit category. http://sims4studio.com/ S4S is free you only need to register to download it.
I hope this helps you somewhat with your CC.