Reproducible research depends on having good systems for organizing and documenting your research. These resources provide recommendations for setting up and maintaining well-organized projects.
There are a lot of things to document as part of your research! If there is a metadata standard for your discipline that is a great place to start as it will tell you what to document and how. If not, try writing a "readme" style guide to your data. Read more about metadata standards and see if there is one relevant to you below.