My own project is a little convoluted in its directory setup as its quite large in scope, but I would imagine that this would be a good setup.
My personal recommendation is to define a "cms" or "admin" module that can keep your admin editing in a seperate directory structure from your frontend normal display code. Of course, all this is up to your personal preference.
As such, I would impliment a folder setup per suchly
For my own application I have an init file inside my /appplication/files directory that loads up ZF, initialises user classes, logs people in, database connections etc.etc. I find this to be the easiest and most elegant file structure to use
..../classes -- in here goes any custom classes you might write, like image handling etc etc