Another thing that can help significantly is using creativity. Charting the placement of the minor prophets, for example, can help you graphically identify when they prophesied, providing much greater significance to what they say. It wasn't until I figured out where they were in time sequence that I understood why they said what they did. Creativity helps clear up difficulties. Comparisons and contrasts.
Comparisons help highlight the similarity between things.
Contrasts help us focus on the differences. Take a passage like Galatians 5. In it, Paul contrasts the things that characterize walking in the Spirit and walking in the flesh. By listing those contrasts, we can see just how important the differences are. Another helpful tool as you read God's Word is to record what is repeated.