Bible study starts with Bible reading. You can read without studying, but you can't study without reading. Spend time reading (preferably your printed Bible) every day, and you'll think more clearly and make better progress in your studies.
When you want to take up the study tools you can begin with the main reading page, the Chapters tool. From there you can take notes on what you're reading, ideally with the intent of eventually forming those notes into a coherent study text. When you're ready to write a study use the Studies tool, where you can also read and take more notes. If you want to search the Bible start with the Concordance tool. There you see how the Bible reuses words and phrases in different contexts, and your searching can flow naturally into reading and taking notes. There are other tools, too.
The links below tell more about how this site has computerized the Bible for studying, and mention some areas for future development.
Source Text
Computerization
Natural Language Processing