I believe in the newer versions (I believe since 2.5.1.1) -- the templates are stored at htdocs/themes not at conf/templates or webwork2/themes. (These latter files are not being used at all I believe and we'll remove them permanently once I'm sure of that.)
One of the nice things about the new mechanism is that you can drop a theme directory into htdocs/themes and it appears in the Course Config page -- no editing required. (You might have to reboot the server after adding the theme directory.)
-- Mike