The goal of hologram is to make it easy to document your CSS and to display the code examples to use that CSS. Hologram has no opinions about how you should actually organize/style your style guide. You could do everything as a single file with no header/footer and it would work just fine. Or, you could break it up into an individual file for each component. Top navigation, left navigation, no navigation....that's up to you. Build it however you'd like.
This is a work in progress, please consider contributing to hologram.