Where to put System & Application Folders

Hi All
Forgive me if this is a stupid question but the advice for best security practice is to place the system and application folders above the web root which is no problem. One thing I can't get my head around at the moment though is I am advised to put the Application folder out of the public domain which files do I leave in the public folder for people to access?

Any advice would be much apprectiated for an obvious newb.


-- system folder
-- application folder
-- secure documents
-- public domain
-- -- css
-- -- img
-- -- js
-- -- downloads
-- -- documents
-- -- index.php

something like the above is ok. You leave css, js, images and everything that is freely accessible.
Everything that has to be secured you put above the public domain.

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