Black ink is good enough for all purposes. I use no other, unless it be red ink to draw attention to “the blood.”
The simplest way to mark is to underline the words or to make a stroke alongside the verse. Another good way is to go over the printed letters with your pen, and make them thicker. The word will then stand out like heavier type. Mark “only” in Psalm 62 in this way.
When any word or phrase is oft repeated in a chapter or book, put consecutive numbers in the margin over against the text. Thus, in the second chapter of Habakkuk, we find five “woes” against five common sins; (1) verse 6, (2) verse 9, (3) verse 12, (4) verse 15, (5) verse 19. Number the ten plagues in this way. When there is a succession of promises or charges in a verse, it is better to write the numbers small at the beginning of each separate promise. Thus, there is a seven-fold promise to Abraham in Gen. 12, 2-3: “(1) I will make of thee a great nation, (2) and I will bless thee, (3) and make thy name great; (4) and thou shalt be a blessing; (5) and I will bless them that bless thee, (6) and curse him that curseth thee: (7) and in thee shall all families of the earth be blessed.” In Prov. 1, 22, we have (1) simple ones, (2) scorners, (3) fools.
Put a “x” in the margin against things not generally observed: for example, the laws regarding women wearing men’s clothes, and regarding bird-nesting, in Deut. 22, 5-6; the sleep of the poor man and of the rich man compared, Ecc. 5, 12.
I also find it helpful to mark: 1. cross-references. Opposite Gen. 1, 1, write “Through faith, Heb. 11, 3”—because there we read—“Through faith we understand that the worlds were framed by the word of God.” Opposite Gen. 28, 12, write—“An answer to prayer, Gen. 35, 3.” Opposite Matt. 6, 33, write “1 Kings 3, 13” and “Lu. 10, 42,” which give illustrations of seeking the kingdom of God first. Opposite Gen. 37, 7, write—“Gen. 50, 18”—which is the fulfilment of the dream.
2. Railroad connections, that is, connections made by fine lines running across the page. In Daniel 6, connect “will deliver” (v. 16), “able to deliver” (v. 20), and “hath delivered” (v. 27). In Ps. 66, connect “come and see” (v. 5) with “come and hear” (v. 16).
3. Variations of the Revised Version: thus Romans 8, 26 reads—“the Spirit Himself” in the R. V., not “itself.” Note also marginal readings like Mark 6, 19, “an inward grudge” instead of “a quarrel.”
4. Words that have changed their meaning; “meal” for “meat” in Leviticus. Or where you can explain a difficulty: “above” for “upon” in Num. 11, 31. Or where the English does not bring out the full meaning of the original as happens in the names of God: “Elohim” in Gen. 1, 1, “Jehovah Elohim” in Gen. 2, 4, “El Shaddai” in Gen. 17, 1, and so on.
5. Unfortunate divisions of chapters. The last verse of John 7 reads—“And every man went unto his own house.” Chapter 8 begins “Jesus went unto the mount of Olives.” There ought to be no division of chapters here.
6. At the beginning of every book write a short summary of its contents, something like the summary given in some Bibles at the head of every chapter.