i personally don’t understand why people highlight in different colors either, but i know it’s also subjective! you can study by reading passages and noting questions that you have, or study with a theme in mind. like themes of light or themes of subverted worldly standards/expectations. try not to worry so much about how other people are doing it because there’s not really a wrong way. i know there are tons of online resources too that can be really good study guides
i use an ESV that has lines for notes in the margins, and that is super helpful for writing down thoughts and questions. i’d probably start with a book like Mark and look for themes within the stories. especially noting which kind of stories get sandwiched together, and what the writer placed in the middle of those