Lyx has convenient change tracking features, graphic format conversion, and spell check, making it a nice front end to Latex. Here I have posted a Lyx skeleton file to start a thesis. Most of the preamble settings should work as is so all you need to do is edit the commands in the top level file, and write your thesis in Lyx. Obviously this file comes with no warranties or guarantees.
Lyx thesis template download
A template for use with Lyx is available here: suthesis-lyx.zip. Top level document is thesis_toplevel.lyx. Modify this document with your own information. Default settings are singled sided and 12 pt font. Change these settings in Document->Settings. Change latex options in the preamble section. Add additional suthesis as ERT (evil red text, raw Latex code) in Lyx.
Included as an example are Abstract, Acknowledgements, Chapter1 and Appendix1 sections. Bibliography is included using jos.bib as an example.