Question about mods in general and mod folder

I see some mods say to put files in the corresponding folder under my games (for example items, units, etc..). Other mods say just drop it in the mods folder. My question what should be the directory structure inside the mod folder? Is it like SOSE where you need a folder with a mod name and the same folders within (ie units, items, etc..) ? I've tried just dropping them in a mods folder (and enabled use mods) but it hasn't worked for me. Putting them in the corresponding folders one directory up from the mods folder does work, but now that i've downloaded a bunch, I want to keep things neat. So is it 1, 2, or 3?

(all under the My Games path)

1)

Elemental

    Units, Items, Etc..

    Mods

        Items (in here goes files depending on what is modded)

       Units, Etc...

2)

Elemental

    Units, Items, Etc..

     Mods (in here goes all xmls)

3)

Elemental

    Units, Items, Etc..

    Mods

        My Mod

              Items (in here goes files depending on what is modded)