If a mod has been deployed into a subfolder of your
\Mods folder, then it's expected that you'll use the "Character Folder" approach. This means that you'll tinker with
CharacterFolders.txt and
Mods.txt files, as described in the
Newbie Guide. Once this is all done correctly, the mod will appear in your character roster (alongside SD Chan, Asuka, Rei, etc) and the mod can be activated by clicking on its roster entry.
If you
don't intend to use the "Character Folder" approach, then there's no need to keep all of the files in separate subfolders. You'll need to move the settings files (such as
animtoolsV21settings.txt,
penisrangeV4settings.txt, etc) into your
\Settings folder. You can move all of the SWF files into a single folder for convenience, or just leave them in their current positions.
Please note that there's a special Character Folder named
%INIT%, which is also described in the Newbie Guide. Mods can be installed into that folder and then they'll be activated
automatically whenever the game launches. This is a convenient way of handling "baseline" mods which you want to be active throughout your gameplay experience (such as
animtools,
moreclothing,
dialogueActions, etc).