Found out today that the style guide my university is using for dissertations is,
A Manual for Writers of Research Papers, Theses, and Dissertations, Seventh Edition: Chicago Style for Students and Researchers
Downloaded it to kindle and read through it. It has some excellent chapters on conducting research. Although I have already been working on methods for cataloguing my annotations, I found the chapters on this refreshing to consider. Also, it includes chapters that would be useful at all levels about formulating research questions and I like the templates it provides for formulating research questions. Would be interested in hearing other people thoughts you have used this guide before.