If your ColdBox layouts are in an external location, you should be able to use the layoutsExternalLocation setting to find them.
As far as static assets like JavaScript or CSS, those are requested directly by the browser and will require a virtual directory or alias in your web server (IIS, Apache).
I have one for /js, /css/, and /sharedImages which point to directories of the same name in my common folder.
Thanks!
~Brad