No unfortunately it will not work what follows is how to do it properly taken from our team pages tricks section.
06:. I have a Dual Processor machine. Am I able to run Multiple instances of F@H?
YES! Absolutely, just run the install program twice and make sure to specify different directories. Now go the Shortcut's for the console and change the target line to read like this.
"C:\Program Files\Folding@Home\fah.exe" -local Click apply and click ok, now start up the Consoles, by specifying local you are telling each folding installation to get it's own unit's to process otherwise they will process just the one. This step is important!
If you already have your Folding@Home client setup once you run the install again to install it into it's own directory and THEN you copy the fahclient, opls.prm and client.cfg files into the new directory you created. And that should be all you have to do to run F@H SMP
You may still run one copy without the -local flag, and it will use the installation directory, but do not run simultaneous copies of Folding@home from of the same directory - they would interfere with each others data and not accomplish very much.
Hope this helps!