This was an odd practice for me to get into. In Judaism, to mark anything on the Bible was considered a desecration! Christians on the other hand do it all the time. I don’t think God considers this a sin… rather, a tool for all of us to be involved in!
There are a million schemes for it – you just have to find what works the best!
Minimal: This is the most common one, you just underline something that means something to you.
Alternating: I used this one for my hardcover Bible. I had four markers, and the system was fairly simple. Green was anything bad, then I alternated the next three colors. That way it wasn’t one big blob of one color on a page.
Systematic: David Cloud writes of this manner. You just have to determine what’s important. For instance, circle the verse number for each of the ten plagues if egypt. Underline Generations throughout Genesis. Circle the words “Day” in Genesis 1-2. Pencil underline every time the author refers to himself in an epistle. Highlight the word Hell in the gospels in Red. Use different colors for different things in different books. This way you can use 66 different meanings for a circled verse number, and you’re not trapped into something that may not work, or be too complicated.
Margin notes. DON’T write down notes on the Pastor’s Sermon in the margins of your Bible. It takes a lot of whiteout to remove those later. Trust me! Instead, get a Bible cover that comes with a notepad in it, and use that to write down notes on the sermon.
DO write down cross references. I’ve taken my hard cover bible and made notes on answering Jehovah’s Witnesses. I’ve written down cross references to share the Gospel. I’ve written down other passages that seemed to me to be speaking on the same subject.
Find what works for you, and don’t feel trapped you have to choose one system!