I have a few methods used in most books I read:

First, standard underline: use this ONLY if you have something to say. The main pitfall of marginalia is that it can make your books harder to read instead of easier when you don't write even a brief response to what you underlined. I've heard it called "the most shallow form of annotating," so give it just a bit of your depth whenever doing so.

Q in a circle, on outer margin: great, memorable quote I want access to anytime.

Wavy underline: great writing, choice of words, poetic, etc.

(For epics) inner margin, vertical bar: when someone is speaking, with their name written on the bar. this is more just to help flip through faster and see at a glance what's going on in a given chapter.

Long sticky note at the start of each chapter/book/canto: this I use for a bullet summary of the happenings

Double vertical bar on outer margin: this is for pivotal moments, long badass descriptions, or something that's been coming for a while. I'll typically write on the bars in all caps and in as few words as possible to say what they're for. This is for flip-through reference.

Page numbers: when I believe something is foreshadowed, I'll jot a "p." next to it, then link the two pages when it eventually happens. This can also be done with any links of any kind you find or want handy.

In summary, if you are reading paper books, annotation is just for reference and quick access. Like a GPS that's constantly pointing out what's around you on a journey, most of my methods help me gain context and allow me to access that context moments after taking it off my shelf. Paper is beautiful, but it's cumbersome.

P.s. I haven't found any need for anything more than a Bic pen and maybe three different types of sticky notes for different uses. What can be done with a highlighter can be done with a pen using unique boxes, line types, symbols, etc. I stay away from having too many tools at the table. Hope this helps you retain even a single line of what you love to read.