I believe that IS your actual desktop... the highest (or lowest) level you can go is root, which is merely /. ~/ indicates your user folder; something in ~/Desktop is in the desktop folder of your user account, which should be what you see on the desktop. Does the file not appear against your background?
The directory ~/Desktop and the background do not share the same Finder layout and view options. The contents are the same, as expected. I am looking to alter the background layout.
This is something that REALLY got me mad when I was using OS X... I mean, I love to write Scripts that are moving stuff and the like and when I tried to record let's saya script to place the icons back, it didn't work... Grrr...