Havergal was an avid student of the Bible. It is said that she had memorized the Gospels, the Epistles, Revelation, the Psalms, Isaiah and the Minor prophets. In addition to that she had studied Greek and Hebrew. As a result of that knowledge, her writings were based on deep Bible study and included many Bible reference annotations.
In some of the Memorials editions, one finds a helpful appendix which includes information on her Bible study. Some of that information is contained on this page.
The following page from her Bible reveals how she took notes as she was reading.
Here is the instruction she sent her neice Cecelia relative to Bible Study. Following the instruction is a fly leaf from her Bible that reveals studies she had made. This comes from the 1880 edition of the Memorials.
"It is at our brother Frank's suggestion that the accompanying facsimiles have been taken from my sister's Bible. She had thus referenced two of Bagster's Bibles, the Old Testament, as well as the New, showing her diligent searchings. Truly, her delight was in the law of the Lord, it was always her standard of appeal; and, by comparing Scripture with Scripture, she grasped its all-sided truth, rejoicing therein as one that findeth great spoil." To her niece Cecilia she wrote:
"In reading the Scripture it is best to combine plans. Once a day read straight on, with prayer and careful referencing. But always try to give a half hour to Bible study; work out Bible subjects, and make notes of them. I will give you two or three which I have found profitable.
"Everlasting." Search out and classify the places where it is used. (This is very comforting, "everlasting covenant," "everlasting joy," etc.)
"Called." (How is our "calling" described? Unto what are we "called "?)
"Keep." Who will keep? Whom does He keep? From what does He keep?
"Able." (See how applied to Christ; arrange in order.)
Keep a fine steel pen on purpose at hand, and mark the references you thus find in your own Bible, this will greatly enrich it. . . . This plan is very helpful, both for intellectual and spiritual knowledge of His word.
The other facsimile is taken from one of the fly leaves of my sister's Bible, and shows the way in which she constantly arranged Bible teachings.
Memorials, (London: James Nisbet & Co., 1880), pp. 277-278
To really appreciate her method of Bible study I would encourage you to read through "All Things," a presentation which she gave to a YWCA in 1879, and was based on a study she made in the Scriptures of that phrase.