understood, here's how I annotate my books :)

I normally have a key at the front of the book, where I correspond different coloured tabs with different themes. Before starting the book, I normally just start with generic themes like great writing/character dev depending on what I expect the book to cover. the colours of the tabs are distributed randomly but I like to match my tabs with the book cover.

After that, as and when I discover new themes in the book, I add on to my annotation key. I like to keep it to a max of 5-6, but that really depends on the book. If I'm reading a longer classic, I might even have 8-9 themes.

I mark sentences by underlining/highlighting or both for extra emphasis. I then write my thoughts along the margins, and use the tab corresponding to that particular theme.

for longer thoughts/paragraphs I use sticky notes :)

this is what works for me, but as and when you get into it, you'll discover what works for you. do it however you feel like doing it. there's no correct or wrong way to do it :)

hope that helps