We advise to write your thesis using LaTeX.
To simplify your life we have prepared a template consisting of two files:
The main file thesis-main.tex contains all basic settings and the overall layout specifications.
The section file thesis-section01.tex is an example for a file containing one section of your thesis. It contains some examples and may serve as a basis for all your sections. These files are read by the main template file.
A further file for title stuff shall be added later.
This setup provides already a lot of sophisticated stuff, just look in the code and use whatever seems appropriate.
They are based on the class cc which is part of several distributions and the package computational-complexity available at CTAN. Beyond that we like to use a set of styles providing several often needed functionalities. Some are mentioned in the template, just remove the comment signs to use them.
Most used by ourselves are these styles.