By all means, the Bible and scripture inside are so fragile, and they always require special handling. Thus, you should check the highlighters before you will cover the main text with them. For example, you can highlight a piece of text with some pens on the small piece of paper at the end of the Bible. If it works nicely, i.e. it doesn’t bleed through the paper and totally close the text, then this highlighter is a good option.
Then, you should create a color system, for example, for identifying who the God is – use pink, for things related to Christ – use green, for the meaning of sin – use red. This identification will help you search for a particular part very quickly and connect it to other important things said there.