I'd suggest you delete your fledgling layout file (you were on the right track, but you need more detail than just the header), then have a look at the LyX layout file provided at http://www.scss.tcd.ie/Eamonn.Linehan/code-latex.php. Modify Dr. Linehan's layout file to point to your thesis .cls file (and of course give it the same file name as your .cls, with .layout extension) and see how far you get. You'll need to edit the layout file to get it to conform to your class (and get rid of any features that your class doesn't have), but it's likely to get you moving in the right direction.
/Paul
