I don't think you are missing anything.
My limited experience is that the desktop in enlightenment is kept nice clear as a work surface
If you want applications (and their icons) to be ready & visible you put their shortcut icons in the ibar
(currently you will maybe have the pre-set ibar with icons for firefox, pidgin, gimp, terminal, thunar
and a few others) which sits next to the start button... you can of course change those listed to your own favorite applications.
While files are accessed are accessed directly through the file system via thunar or konqueror or dolphin
or whatever file system you use. You can create short cuts under under to thunar but not to your screen desktop but rather to a desktop that sits near the top of your personal user file system.
this probably does not make alot of sense...just trying to figure it out myself..so someone please correct me
I like the uncluttered approach
in other OSs I am likely to have a very messy desktop