First, let me say that there is no right or wrong way to study. Do what works for you.
The first thing I do before any study is pray. Ask the Lord to open my eyes, show me direction, give me wisdom, help me understand His word.
I then create a cover sheet. This is the who, what, when, where, why and Who of that book.
I then apply the S.O.A.P. method to a key verse. (Scripture, Observation, Application, Prayer)
I then go verse by verse of the book I am studying. I write down what stands out to me. I compare my translations (NLT) to the (KJV) and define words that stick out or that I want to understand better. I use a Strong's Concordance for this. If I feel the need, I might write down a prayer or something I feel the Lord is saying to me that I can apply to my life.
Verse mapping is a neat way to dig into scripture and really define it. You get a better idea of what that scripture means.
How does it work? (it is really easy, I promise)
1. Find a scripture or passage. Anyone will work.
2. Use your everyday translation of the Bible.
3. Mark words you want to define.
4. Define these words.
5. Re-write the scripture, but this time replace the words with their definitions.
6. Write a summary, prayer or what you think that scripture is saying.
7. Write the same scripture in at least 2 other translations.
8. Write down any cross references for this scripture.
Here is one I did on Micah 7:7 (using the NLT translation)