Use the portable version of calibre (or you could do one native install and one portable). You can even store them on the same partition, the folders just have to be named differently.
calibre-portable:
http://calibre-ebook.com/download_portable
Download the above and unzip to the folder of your choice and name it Calibre1, then unzip it again this time, name it Calibre2. Voila, you now have two versions installed. Of course, this only works on Windows.
What exactly are you trying to accomplish and why do you need two versions anyway? More info would be helpful to make sure the set up would work as you want it (I actually have more than 10 instances of Calibre installed on my PC that I'm playing with).