Make notes as they occur to you about the connections. Show your diagram or map to others, see if it makes sense to them. Ask for suggestions. If one sort of diagram doesn't make sense to you, try another. Use a hierarchical diagram, or a network, or turn the pictures you've drawn upside-down to get another perspective.
Concepts become sections and pages.
Connections becomes links. If links are very strong, consider joining the sections into one. It is worthwhile to take your time structuring your web presence, because the way your web pages are put together is itself information, and is crucial to how the presentation is understood. The best web pages are clear, concise, and well-organized. Once you have a map of your presentation, you can begin work on specific content.