Dr. Al Mohler has written on “How to Use a Study Bible”.
From his article:
1. Read the text of the Bible first. Meditate upon the text and read it with care. Apply your own knowledge of the Bible in order to understand the particular text within its context and place in the biblical story-line. Consider and note other texts that come to your mind as directly related to this text. Read the text with full attention and conviction.
2. Look carefully at the cross-references that the study Bible links to the text you are reading. Do not look only to the citations, but read the actual passages. This assistance is still the main contribution of a study Bible — making related and parallel passages more accessible. A first principle of interpreting the Bible is to interpret the Bible by the Bible. In other words, to allow the Bible to interpret itself text by text.
3. As a third step, take full advantage of the notes, articles, and other helps printed alongside the text. In some cases, short articles will help in understanding contested issues or matters that might otherwise require a Bible dictionary or encyclopedia. Where appropriate, maps can be very useful, along with tables of measurement and similar points of reference. The very best of the study Bibles will also offer some level of commentary within the notes.
Read the rest of Dr. Mohler’s article.