The obvious way of using folders is to arrange the elements that make up your Google Earth file as if they were browser bookmarks or files in windows explorer. However, there is another way - using folders as picture frames.
By Picture Frame I mean that you arrange a number of items that make up a logical view and put them in a folder. You could also think of a picture frame folder as a map. With a paper map layers cannot be turned on and off, this can be achieved with folders by deselecting the 'allow this folder to be expanded' tick box in properties.
This is a screen shot of a project where I did just that. I created the 'Chine Development' folder and selected the 'show contents as options' tick box in properties. I then created a number of folders each with a some elements (placemark, overlay) inside that made up a 'picture frame'. The radio buttons you can see alongside the sub folder icons tell you that only one of the sub folders can be selected at once and I made it so that sub folders cannot be expanded.
I've posted before about needing to convert the tour of this project to a video, however, the folder structure shown above works just fine to create picture frames. Maybe picture frames are a good way of presenting the best of your project? You could cherry pick your data, arrange the data elements into picture frames and publish a set of them as a data summary (rather than an introduction which you should have as well). The rest of your data could be published separately for the power users to explore.