In the image below, you can see how folders can help you organize your Plato folder, making it easier to find files that need updating, and preventing files with the same name from writing over another file. For example, this user has an index.html file for his or her main opening page, and another index.html file for the opening page of a collaborative project file. Such files are good for opening pages, because they do not have to be typed into the URL for the page. The main Plato page opens such an index file, but only needs this URL: http://plato.mercyhurst.edu
Whatever organization you use, it pays to think about it and even sketch it out in advance.