I keep mine in their own folder.
I have one mod by Sacrificial, and it's necessary to keep his mods, each in their own separate folders. I do the same for the others, with a few exceptions. Those small mods that's one file, only, I keep just inside the Mods folder, itself, the same for the various transcript files.
I have since organized my Mods folder. Since I have some items to represent the 18th century, I group them by gender and clothing.
18th century Women Clothing
18th century Women's hats
18th century Men's Clothing
cc Decor
cc Hair
Name of Mod for each mod.
This makes it easier for me to pull certain cc or mods from the game when trying to track down what's causing a problem in my game. and it's just tidier.
I also label each folder with the name of said mod and the version of it, so I'll know if I have the latest update.