Interactive media projects are like icebergs. 90% of the work is invisible in the final product. You may think that you can keep all the components of your current projects organized in your mind. But a time will come (sooner than you think) when you can't. You may think your linking architecture is perfect, until you demo it and realize that several segments make little sense.
The storyboarding of a complex project before you begin to create your screens:
1) Take some time for preliminary planning. You should know roughly what you want to do/say/demonstrate/illustrate/argue/advocate/etc. before you begin your storyboarding process.
Your content will inevitably influence the forms you choose to communicate it. But allow yourself space as you storyboard for the form of production you choose to influence the content, too. You may need to carry out more research (on content) and development (on techniques - however simple- you want to learn), for example, after you storyboard.
2) Take one sheet of 8.5 x 11.5 paper for each screen you plan. Before you begin to compose each storyboard, turn your sheet of paper sideways (landscape orientation). Remember that the screen on which your work will appear is wider than it is tall and you need to design your textual media with this in mind.
3) Using each sheet of paper as the template for one screen of your hypertext, design the visual and textual elements of each screen. You may need several pages for some screens as you script out visually elements that change according to reader/viewer input. Name your screens, and the elements in your screens, clearly as you progress (saves a lot of time at the assembly and posting stages).
Don't forget that each screen is both a coherent textual and visual work of art on its own and a single element in a wider narrative. Play with and against audience expectations, depending upon your purpose and audience.
4) Experiment with architectures for the linking of your storyboarded screens. As you are working in a spatial medium, use space to help you design your architecture. Pin your screens on the wall, or spread them out on the floor. Build a flowchart...
...and then take it apart and create a new one. And do it again. And maybe again...
5. Commit the most final of your provisional navigational structures to a sheet of paper.
6. Submit all your storyboarding material for grading on 15th October.
7. Review comments.
8. Implement online!