@NitzanHavoc
Well, if you follow those rules you set up, you won't have a problem when it comes to location. But you have a little more leeway than that.
Any files with ".ts4script" at the end can go into folders ONE folder deep.
Any files with ".package" can go into folders 6 folders deep.
There IS something to be said for organization. Especially since every time the game updates you will need to go through ALL your mods and check for updates. It seriously helps if you keep them well organized.
Put CC in a single (nested) folder since those rarely break with updates.
Put Like CC together: decor, clothing, hair, etc. Makes it easier if something like "tubs" breaks, you don't have to go through 10,000 cc files to find your tubs. 🙂
Keep mods from the same creator together so when you check them for updates, they're all together. (Note the script mod limitation)
* One tip, if the mod has a version number, put a text file in the mods directory next to it with the version number in the file name, that makes it simple to verify what version you have compared to the one on the mod author's website. If the mod doesn't HAVE a version number, then use the date it was released/updated!
Organization is imperative, especially when you have a LOT of mods/cc. I have close to 14 gigs of CC/Mods in 4,000 files and patching/updating is a snap for me.