Writing a thesis is considered by just about everyone to be a lot of work. Here is some information to help you avoid common pitfalls of formatting.
This is not meant to be an exhaustive list, but covers some of the items that seem to come up again and again. What everyone wants is to put their thesis together as painlessly as possible so that the science is clearly conveyed.
First of all, the Department office (room 3302, Joanne Martin) has the thesis of each graduated student, so you might want to take a look at past examples.
Please note that the official name for the graduate school is "Faculty of Graduate and Postdoctoral Affairs". The old name was "Faculty of Graduate Studies and Research" - please update any template that you have to the current name.
The best style manual that we know of for physicists is at http://www.aip.org/pubservs/style/4thed/toc.html particularly with respect to grammar and how to format a decent graph.
the figures too much. Keep them at a good size. People have to be able to read the lettering and distinguish the curves. An advantage of the thesis is that the figures will not be miniscule the way they are in a journal article.
reference for the source - the title page of your thesis declares copyright for all this material under your name. Sometimes material, especially in particle physics, is overtly in the public domain. If you think that's the case, please verify it, and if so then it's your lucky day! Otherwise, you have to get permission from the publisher of the journal or book from which you want to reproduce material. Ask yourself if you really need to reproduce the material, or if a simple reference will do. A graduate research thesis is different from the reports many people have written earlier in the education system. There are strong reasons why we reference things, rather than reproduce them.
It's not a formal requirement, but most theses in Physics are made more user-friendly by having a Table of Abbreviations or a Table of Symbols. It helps the reader to have a page to check acronyms like NLO, VBF, COMS, HDR, LET, BDT, DVH etc. and/or check mathematical symbols.
That's a lot of scientists and the problem is not going away soon no matter how good our computer technologies get.
line weights to distinguish the two lines, or simply label the two lines directly with arrows. Using colour for the lines is unnecessary.
Example 2: when a CT image must be overlaid with a PET image, one of the best ways to distinguish the two images is to use colour. e.g. make the CT greyscale and put the PET in colour. The colour allows the viewer to separate the two types of information despite their spatial superposition. It would be almost impossible to do this without colour.
The section near the end where you list references is properly titled "References" not "Bibliography". A bibliography generally is just an unordered list of general reading. If you are using a template that titles the section as "Bibliography", please change it.
Note that the good acid-free paper is not needed until after you've made the corrections following the defense. And when you do get to that point, two of the copies can be on regular paper, with the rest acid-free.
If you are unsure about something, there are a lot of people around who can help, including faculty plus other students and postdocs in your group. Many many people have laboured through the task you now have at hand. And again, take a look at the theses in the Departmental office.