There is no need, I think.
You can easily switch between two installs, if you want.
Install your first copy.
Suppose it goes into D:\Steam\steamapps\common\skyrim.
Now go to that folder.
Rename the skyrim folder to something else: e.g. skyrim.play
Now install Skyrim again.
Steam (or the dvd install utility) should notice that the skyrim folder is gone.
It should just reinstall a fresh copy of the whole skyrim game.
Now you have 2 installs in D:\Steam\steamapps\common, skyrim and skyrim.play
Whenever you want to switch, just rename the folders, so the one you want is called simply "skyrim", and start the game.
If you need separate ini-files and saves files, you could do the same thing with the My Documents\My Games\skyrim folder.
You could make a simple old-fashioned batchfile to rename the folder with one click.
I haven't tried this exactly myself though. But I've done something similar early this year.
I think it will be easier than making Steam believe you got 2 copies of Skyrim.