Thesis Template
I wrote, formatted, and edited my thesis using TeXworks, a free, open-source TeX editing software. (You can download it and all necessary associated files using that link.) The formatting used in these documents was accepted by the Graduate School in August, 2014, but you should probably check if there are any changes in the requirements.
what do the different files do?
spelling
For keeping track of references, both for the thesis and in general, I recommend Mendeley, a free reference manager. It stores PDFs, is searchable, and it creates (and automatically updates!) a bibTeX file that creates handles the references in the thesis.
talk about basic commands \cite{} \label{} \ref{} \begin{equation, eqnarray}
other zip files - for alternative formats