Your research journal becomes a repository for your thinking, a record of your research activities, a place for notes about locations of documents, spreadsheets, and other files, and a place to plan what you are doing next, as I previously discussed here.
Because it contains a mixture of different types of information and can span over more than one notebook, you need a way to link different parts of your research journal so you can find things. Some people refer to this as threading. At its most basic threading involves including a page reference to another section of your notebook in a notebook entry.
Kim Alvarez gives a detailed explanation of different ways of threading in paper notebooks in her post on the Tiny Ray of Sunshine blog here. Her post is useful to look at even if you are using an electronic notebook, in which you will be able to thread using hyperlinks to different sections, pages or paragraphs of your notebook. See here for instructions on how to add these links if you use OneNote.