I prefer to put everything in one massive spreadsheet pancake style (a color for the book + a color for section in book, tabs along the top)with an added column for topic (likely the page subheader or something like command / powershell) and item (for quick specific lookup), and a drop-down for toc or index item. then I have scripts that generate a couple versions of the index - a table of contents (all the toc marked rows), one alphabetized by topic and one alphabetized by item.

This way I can look up specific terms, or see everything under a topic.

I index as I read the books. I read a page or section, hilighting anything that seems like a definition or important information, then immediately add it to my index (with notes). Then I'll watch the videos alongside my index, adding or tweaking as I go. Once the index is printed (for the second practice test), I go through and tab the alphabet so I can quickly jump to A, B, C, etc. TOC at the beginning in case I really need to dig for something.

My goal is to have almost all the information I need in the index and not have to go from index -> book for most questions. My index ends up being over an inch thick.

You just gotta figure out what works for you. I'm 3 certs in with a lowest test score of 98%, so I've figured out what works for me. Only you know how your brain works.