Let the Holy Spirit be your guide.
"However, when He, the Spirit of truth, has come, He will guide you into all truth" (John 16:13) We should always pray before we begin studying the Bible. Something like, "Dear Lord, open my mind to see what you have in your Word."
Come to the Bible with the spirit of a child.
"You have hidden these things from the wise and prudent and have revealed them to babes" (Matthew 11:25) Don't come to the Bible to prove your own ideas or prove other people wrong. Pray something like, "Lord, I'm coming to you today, not to superimpose my will on the text, but I'm coming to you so you can speak to me through your Word."
Let the Bible interpret itself.
Let clear Scriptures interpret unclear ones. "Whom will he teach knowledge? And whom will he make to understand the message? Those just weaned from milk? Those just drawn from the breasts? For precept must be upon precept, precept upon precept, line upon line, line upon line, here a little, there a little" (Isaiah 28:9-10)
Build no doctrine on just one or two verses. Get all the Bible verses on a subject. Remember the fence post principle.
With just one fence post, you have no idea which way the fence is going to go. With two, you have a line and get a clearer picture. When you get 10, 20, 30 fence posts, there is absolutely no doubt where that fence is pointing, then you have clear truth. Each Bible text on a subject is a fence post, you must look at all of them together to get the clearest picture of where the fence points. (see Isaiah 28:9-10)
Use the right tools.
Every good Bible student should have a concordance. One example is Strong's Exhaustive Concordance. A commentary can be helpful, but always remember it is only the opinion of a man (or woman). If you come across something in a commentary that is out of line with Scripture, the Bible gives advice: "Cease listening to instruction, my son, that will lead you to stray from the words of knowledge" (Proverbs 19:27)
One helpful tool while studying the Bible is an idea from Mark Finley. He uses the acronym VIM. As in, "study the Bible with vim and vigor."
"V" stands for visualization. As you read the stories in the Bible, visualize them in your head, try to paint a vivid picture in your mind of what is going on.
"I" is for identification. What would it have been like if I was one of the characters in the story. What would I be thinking or feeling, hearing or seeing.
"M" stands for meditation. Really think about what the story means. What truths can we learn from the story, and how can I apply it to my life.
Be willing to follow whatever God reveals to you.
"If anyone wants to do His will, he shall know concerning the doctrine, whether it is from God or whether I speak on My own authority" (John 7:17)
Some of these ideas are from Shawn Boonstra's booklet, The Sword of the Spirit, thanks to It Is Written.