Instead of using the thesis template available on the SGS Website, you can use a template composed by one of the graduate students of the Department of Mathematics at the University of Toronto. It is based on the classicthesis LaTeX package by André Miede and Ivo Pletikosić which produces a nicer layout. The template is based on v4.6 of the classicthesis package. The introduction of the package manual explains why it typesets things the way it does.
Besides simplifications, some slight adjustments were made to fulfill the University of Toronto School of Graduate Studies style requirements. It also includes some adjustments for better integration with the ams packages and for letter sized paper.
Have fun with the template!Download: Thesis Template
Any suggestions and comments are welcome via email to fparsch at math dot toronto dot edu.
Classicthesis is included in most LaTeX distributions, so probably you do not need to download it separately.