Long ago I got over the idea that I shouldn't write in my books. I'll admit that I only apply this to nonfiction. My fiction remains strictly unmarked.
However, my nonfiction often winds up with a checkmark or star next to significant passages. I don't underline or highlight since that interferes with rereading, as I found to my sorrow soon after I began the practice.
Joel J. Miller encourages even more than my simple system as you may read for yourself. Via Phil at Brandywine Books whose system seems like mine.