Re: Redirecting Program Files and Program Files(x86) in Vista/Win7.
The guide posted here does not redirect the user profile directories, its for moving program files (they have different locations for editing the registry). But to answer your question, if you were to only adhere to this guide, user files, including items saved to the desktop will be stored on the SSD. I assume if you are redirecting your program files folder to conserve space on your SSD, then naturally you would probably redirect the user profile directory as well.
How hard would it be to get this done without a clean install? I have my user files redirected, but my SSD is filling up fast with programs. (I am even considering adding another SSD to get more space).