Hello Katarina!
The number of folders in your project is not limited, and you can use a folder per skin, but you are not limited to it. You could have several skins in the same folder, grouped by kind (e.g. a folder for all hats, or a folder for all weapons) when you add a folder in the Spine project directory, Spine sees them, but they are not automatically added to the project. You can add them using the photoshop to spine script to export their correct position, then using the import function to only add new images: Import - Spine User Guide: Data (this is what I recommend)
Or you can drag them in the viewport through the images node in setup mode: Images - Spine User Guide: Images node
You can nest your skins in subfolders if you prefer, however I think that this is often not necessary, unless for organization purposes, such as having different directions for the same skeleton, and wanting to have a folder for each direction.
If your new skin is a recolor of another skin, therefore all the images have the exact same sizes and names, you can duplicate the skin, then choose Rename attachments to rename each duplicate attachment using the skin and skin placeholder names, automatically changing the path to the folder that has the same name as the new skin name. Skins - Spine User Guide: New skin placeholder
Here's the page about Find and Replace: Tree - Spine User Guide: Find and Replace
What confuses you about it? (:
Thank you for your reply.