[eluser]Fationably Late[/eluser]
I can't really tell you what the purpose of your project is. But if it advice how to structure your files, then I can only give you a few suggestions to get your started. First, you want to think of your directories and/or in one of two ways:
1) Think of them as what an entity
can do:
application/controllers/admin/create_user
-OR
2) think of them as what can
be done on an entity:
application/controllers/user/create
I suggest these approaches because of the 'friendly URL'. But don't try to mix the two or else you're likely going to confuse yourself or your site users in the long run. And there are certainly tons more patterns out there.
If you
really want to separate the cms from the user side, then you should do some research on putting the system folder in a common place and having two completely separate application folders.
I'm trying not to give you direct answers, but merely patterns that people use, because if you don't figure this stuff on your own, you won't understand why you're doing it.