I suspect that you would at least have to somehow install tow completely separate versions of the software, i.e. version 1 to \program files\copy 1 & version 2 to \program files \ copy 2. Even then you'd probably have to play around in the registry and what not to ensure the PC identifies the settings of each separate instance as a completely separate program.
We sort of do this to get dual core PCs running two instances of distributed computing applications, like folding. But most of those have specific file settings, that are made public, enabling the computer tosee that there are truly 2 separate versions runninge, each with their own configurations, logs and such like.
This overclockers thread gives more clues on that.