For those that use a CMS framework to manage a Forrest site, do you edit the generated files or the source files with the CMS application?

I like that with Forrest I can work with source files that are marked up structurally and I don't have to dig through presentational markup to find what I need to edit. Do I lose this if I add, say, Lenya to the equation?

I remember discussion of a Lenya plugin for Forrest. Or was it the other way around? How does that situation look regarding my first question above? I'm interested to hear how people use Forrest with a CMS, such as Lenya or Daisy.

Thanks,
Brian