The CLAS Linux Group have posted this information on behalf of others. This information is likely dated. Use at your own risk.

I would recommend separating your thesis into separate files, much like I do in my skeleton thesis example. Try separating your chapters and appendices into separate files and using my thesis.tex, prelude.tex, newcom.tex, and app0.tex files (customized for your own thesis).

Or, if you already have a system for organization you prefer (perhaps your thesis is all in one file), then make sure you have these commands:
\documentclass[12pt]{report}
\usepackage{uithesis03}
at the beginning of your document (but make sure that \usepackage{uithesis03} is AFTER any other \usepackage statements you have). Then insert your own customized version of prelude.tex immediately thereafter.

Regardless, make sure you issue the \appendix command before your appendices and use the \Chapter and \Appendixcommands (rather than the built-in LaTeX ones) for new chapters and appendices, respectively.