There are many ways to go about writing a thesis and many tools for doing so: MS Word, EndNote, LaTeX, BibTeX, the list goes on. As colleagues regularly use LaTeX for reports, papers, and originally on their own PhD theses there is much more collective experience than for MS Word in this area. LaTeX also benefits from the ability to use version control systems such as Git and Subversion as all the source files are essentially plain-text.
Previously colleagues have used a CUED LaTeX PhD Thesis template originally developed by Harish Bhanderi at the University of Cambridge Engineering Department. This has been updated by Krishna Kumar and is maintained on GitHub with a version 2.0 release. The latest version provides a great deal of flexibility and control over the page layouts but much of the formatting is as required out-of-the-box. Every university will have their own set of “Guidelines for the Submission and Format of Theses” that require slight tweaking of the template settings, but the template is very well documented/commented that it is relatively straightforward to do so.
I have also modified the directory structures a little to provide clearer differentiation (personal preference) between supporting template files and the content sources.
The references.bib file that the main.tex file points to is that as described in the previous post. Both the thesis and references projects having been checked out to neighbouring directories for easy linking.