A year ago when I finished my dissertation at UBC I posted a complete set of LaTeX files for generating a manuscript-based thesis (bibliographies separate for each chapter, etc) in which each chapter is a separate file in LaTeX. (This is useful for being able to compile each chapter into its paper form from the same file.) [Update: 2011: I believe UBC has recently eliminated the manuscript-based thesis option]
But I had given up on the hope of writing the whole dissertation in LyX. I am now posting a (trivial) LyX layout file that can be used with Michael McNeil Forbes’ ubcthesis class to write your entire dissertation/thesis in LyX, rather than LaTeX source code.
So, at least if you are not doing a manuscript-based thesis, you can write it all in LyX. This is all you need:
Download and unzip my ubcthesislyx.zip [Updated May 2013]. In the resulting folder you can, if you wish, update the ubcthesis.cls and genthesis.cls and the other files (linked from the UBC grad studies page). In any case, you can now just launch ubcsamplelyx.lyx in LyX and bingo! You can see the resulting sample PDF.
The trick here is that most of the extra defined stuff for ubcthesis is not dealt with in the .layout file, and therefore by LyX. Instead, most of these definitions come in the LaTeX preamble and are kept for simplicity in the LyX preamble. So visit Document-Settings-Preamble within LyX to change all the front matter settings.
Let me know if you make use of it (or make improvements), please.