Yes I do, of course, and I actually use it nearly exclusively for multi-file projects: I don't write short scripts everyday, but I have bigger projects that need more features. The one I am on: extract data from an existing DB, format it, save it to a csv, send it with SFTP. I build a binary and send it to my servers.
For this I use :ciel as a dependency, I use a typical project structure: a system definition in an .asd file (that :depends-on (:ciel)), and sources. I also start my editor with CIEL's core image. I build a binary the usual way out of this, I don't run this app as a script, specially if I added a couple dependencies. But that's OK, I benefited from CIEL during development.
I recommend to start with a file packages.lisp that defines 1 (one) package for the whole application, to use it across multiple files, until it makes sense to create a second package. Otherwise, one can easily loose oneself into export & import symbols hell, specially when we are new at it. So I don't recommend the "one-package-per-file" approach.
Hopefully the Cookbook gets you covered if you need examples.
I was wondering - do you also use it for larger (multi-file) projects? Any recommendations on how to structure those when using CIEL?