When it comes to designing your PBOK the best thing you can do is start.
Creating an organizational structure for your PBOK requires you to know what you are organizing. You can only know what you are organizing by getting your thoughts and ideas out of your brain.
There are some basic organizational strategies that you should follow.
One is to add as many links and tags as you can. It is easy to remove or rename tags and links later. If they are not there then it is difficult to find what you wrote so it can be tagged.
Capturing and organizing your knowledge will evolve into your personal book of knowledge. It will be organized based on how you think and what is of interest to you. No two PBOKS will be organized the same way.