There is no right or wrong way to organize, but if you're in charge of maintaining the site, you'll want the foundation to make sense to you. Just think about the type of content you'll be dealing with and map out the foundation accordingly. It's better to have short, memorable names, resulting in URLs that make sense, than names leading to URLs that have to be scrawled on two or three pieces of paper. Remember to pay attention to case too. To keep things consistent and simple, use lowercase letters for all folder and filenames.
Servers tend to get confused by strange filenames.
You should also know about relative and absolute links. When you're linking to another file on your site, you might be better off using a relative link. So if you're working on a file called summer.html in a directory called courses, for example, and you want to link to a file called video.html that's in the same directory, you can use a relative link. There are several advantages to using this method. Although it really doesn't take all that long, those little delays can add up, making the user wait and the browser do unnecessary work.