If you are using Linux or some other variant of Unix, it is recommended that you make a directory to hold the above files and other files of your thesis. This may be done using the mkdir command. For example, mkdir thesis will create a directory called thesis. To change into this directory, use cd thesis.
The settings in uw12.clo assume that your thesis will be printed single-sided. If it is going to be printed double-sided, then you need to specify the twoside option in the \documentclass command. Depending on the calibration of the printer, you may need to further modify the lengths \textwidth (line 102), \textheight (line 116), \hoffset (line 217), \voffset (line 218), \oddsidemargin (line 138), and \evensidemargin (line 158) in the file uw12.clo. The settings make the assumption that dvips is configured with A4 paper as the default paper size (which is apparently the case for the Linux machines in the G.3.12 lab).
On lines 7 and 8 of the file uwthesis.cls itself, you will need to change the default settings for the degree and the type of thesis (thesis, dissertation, report, or project) to suit your needs.
Typically, your master LaTeX file, say thesis.tex, will be something like the following:
\documentclass[12pt]{uwthesis}The files chap1.tex, chap2.tex, chap3.tex etc. should each contain a chapter of the thesis. (Of course, you can have other names for your files; just change the above in the master LaTeX file accordingly.) There may well be files containing appendices and a file containing the references. Each appendix should start with the \chapter{appendix title} command, but before the \chapter command of the very first appendix, the \appendix command should be put in (try it with and without the \appendix command to see the differences in the headings and table of contents).
\usepackage{epsf,amsfonts,amsmath}
\title{Pearls of Wisdom}
\author{M.Y. Self}
\begin{document}
\pagenumbering{roman}
\maketitle
\setcounter{page}{2}
\begin{abstract}
The first pearl of wisdom is that people ignore my pearls of wisdom.
The second pearl of wisdom is that people should read the documentation.
\end{abstract}
\begin{acknowledgements}
Acknowledgements belong here.
\end{acknowledgements}
\tableofcontents
\newpage
\pagenumbering{arabic}
\include{chap1}
\include{chap2}
\include{chap3}
.....
\end{document}
The \includeonly command (see a book on LaTeX) is useful if you want to work on just a chapter or two, but you want the referencing and citations to be correct. This command is not as important as in the past because computers are now much faster than when LaTeX first came out.