Hi
@Fuarky -
To answer your question, I would lean towards taking notes on the learning goals and concept checks, because I generally think that less is more when it comes to note-taking, but I also think it's important to emphasize that note-taking is more about you than the textbook. MCAT materials generally provide a fair amount of guidance about what information is especially important -- for example, Kaplan has concept summaries at the end of each chapter that distill the essential material into bullet points. So for it to be worth note-taking, whatever your note-taking process is has to be more useful than just photocopying those pages, stapling them together, and studying from them,
and note-taking has to be useful enough to be worth doing instead of more practice problems, etc. This is why I suggest minimal if any note-taking directly from the textbook.
If you do take notes, I'd suggest focusing more on stuff you don't know and less on stuff you do. Writing down stuff like "the mitochondria are the powerhouse of the cell" and "amino acids are the building blocks of proteins, which are the building blocks of biological life" is not a good way to spend time. Remember that your notes aren't going to be taking the MCAT -- you (& what's in your head) will. So the point of notes is to be a helpful intermediary in the process of getting information and insight from the page or screen into your head. Although everyone's learning style & time obligations are different, and of course you have to make a decision about what works best for you, my general suggestion would be to take very concise notes, if any, and to use the time you save for practice problems.
Hope this is helpful, & best of luck as you study!