Decide whether your journal will be handwritten like a diary, typed up in a word processor or composed online as a blog. Blogs can be shared with a few friends and your adviser, if you have one, which might motivate you to keep on top of your project.
Write in your research journal every day. Note questions that come to mind about what you read that day, thoughts about primary sources and connections between old and new findings. Write down anything that comes to mind, even if it's only how much you dislike your thesis adviser or your roommate. The important thing is to write daily and not to censor yourself; simply free write.
Read through your journal before your start writing your first draft. Highlight crucial points, reoccurring solutions or contradictory findings. This process will reveal the main points of your paper and areas that require additional research, as well as provide leads for future research.