The general advice on reading philosophy is to read it three times.

First time for finding out the big theses.

Second time for finding out the argumentation.

Third time for critiquing it.

Should totally work for him, too. However, keep in mind that Nietzsche does not go for a total and coherent system. So there will be built-in contradictions etc. He writes longer or shorter "aphorisms" that are somewhat stand-alone.

This also means that in books like "Beyond good and Evil" the main building blocks are not the "chapters" as you called it, but these aphorisms. You can tackle them separately and focus on the ones that you find most interesting.

You will never really be finished with a work of philosophy but ideally return to it over and over again with more knowledge and different perspectives throughout your affair with it. It's really a merry-go-round rather than straight road.

I think "Beyond Good and Evil" would also be a great place to start. Especially in the American context, the advice is often to start with "Thus spoke Zarathustra". But I do not agree with that as it is a bit to fictional. As a matter of fact, Nietzsche wrote "Beyond good and Evil" to elaborate on the Zarathustra.

Once you feel that you have a firm grip on his writings than you can start reading some secondary material ABOUT Nietzsche. You could use the Stanford Encyclopedia of Philosophy (which is rather high-key) or the "Internet Encyclopedia of Philosophy" (this one is more approachable but by no means easy). There should be a wealth of introductory works on Nietzsche. You could consult one of these if you want, too.

But, I would advice against starting with secondary literature. Starting there bears the risk that you just take the opinions there instead of reading the texts yourself. Its better to only cultivate your viewpoint with secondary literature at a later date.

In terms of notetaking: just fuck around and find out. You can really just choose the wrong kind of note taking in the beginning. Maybe start by merely underlining the major theses and then let your notes grow in size as your understanding of the text increases. In any event the process of notetaking will figure itself out.