There’s nothing inherently wrong with using the VEX engineering notebooks. You’re not going to lose any points or miss out on sections of the rubric because you used the VEX notebooks. However, I think there are some better options out there if you are willing to pay some more for them. I personally have been using the Design Notebooks sold by BookFactory. They have hard-back binding unlike the VEX notebook, and the general construction of the notebook is very high quality, including the binding and the paper. Personally, I really like how the paper responds to gel-pen ink. The paper accepts it well, which is very useful for sketching designs. You can get them either from BookFactory’s website or on Amazon.
As for your question on documenting code:
Why does the fact that something changes over time mean that it is hard to document? Your robot is never expected to be perfect from the get-go. The entire purpose of documentation of anything from design to building to programming is to clearly document how things change over time. Your notebook is not so much a guide to your end robot but a record of how you got there. As such, I think the best ways to document code is to explain algorithms and processes you’re employing (with the help of flow diagrams or control structure diagrams), include any pseudocode you or your team used, and then paste in a copy of the methods/functions you write based on the diagrams and pseudocode. Including well-commented code here helps explain things even more. In general, use your notebook to explain your thought process in writing the code-- why did you choose to do it a certain way? Why is that better in comparison to other methods? etc.