This is a collaborate effort to establish a UOIT LaTeX thesis template. Currently this template is being created/maintained by M.Sc graduate students, which is why this template is geared towards them).
It is highly recommended that you use a Unix based operating system.
As for actually editing your thesis you can use a LaTeX program (i.e., TexMaker) or simply any text editor.
With preference to a text editor you can use the awesome latexmk script to handle auto-compilation upon saving any part of your thesis. The following is how to invoke the script from command-line:
latexmk -pdf -pvc -silent -r .latexmkrc thesis
The aforementioned command should be executed within the src directory of your thesis. This command will create a PDF of thesis every time you save any part of it. The -r .latexmkrc is required as this template makes use of the glossaries LaTeX package for handling abbreviations (it is required to run the makeglossaries thesis command between each compilation, which is automatically done now due to the configuration in .latexmkrc).