Part of the reason for marking in a book when reading is to be able to reference it later. Here is my way of marking. I have gradually come to this way of marking, but this system is simple and seems to be helpful.
1. I always underline important concepts. I have found that this is the quickest way to reference when thumbing through a book later on.
2. I use an asterisk [*] in the margin next to sections/sentences that are important to the author’s argument.
3. I circle or box (I use these interchangeably) section headings and subheadings (either numbers or words, whichever is more clear when reading). I also use this for particularly important in text phrases, etc. I have thought about using circles to denote major headings and boxes for minor headings, but so far what I have been doing has been fine.
4. I use an exclamation point [!] in the margin next to a section/sentence I found personally helpful, convicting, etc.
5. I use a question mark [?] in the margin for sections that I don’t fully understand, or still have questions about.
6. I generally write “hmm…” in the margin next to sections I tend to disagree with, but about which I have not yet decided.
7. I write “No” or “Yes” in the margin to denote disagreement or agreement.
For all my margin markings I also draw a vertical line (or bracket), so that I know exactly which part of the underlined section the marking refers to.