nowthatweareseparated.neocities.org
Never used that software personally, but it looks like a niche game engine to build a specific type of web game. Learning how to make web games will teach you javascript, but it's gonna be very advanced. I would start with just adding interactive bits to regular websites first such as client-side form validation, making a site theme selector, a hambuger menu to collapse the site navigation into on mobile screens, etc
i keep mine in a css folder, there's really no wrong way to handle it, just make sure that when you reference the style sheet that you reference the folder it is stored in if you choose to do it that way!