Since your processor only has one Floating Point Unit, and most of the work is done by the FPU, you will see very little advantage. Pandegroup actually prefer that you don't run a HT processor in this way.
If you really want to run 2 copies you can do so:
You have to make a completely separate folder for each copy.
Create a new folder (call it something like Folding2) and copy just the console executable into it. If you copy anything else it may not work.
Now start a command prompt, change to the new folder, and run the console program. There will be no config file so it will think this is the first run, consequently it will automatically run the config. I've never found the need to use the -local setting.
It will ask you if you want to change the advanced settings as part of the config. The only thing you need to make sure is different is the machine ID - set it to 2. It will also ask you if you want to install it as a service - it's a good idea to do this.
If you decide to install it as a service, you should stop the program immediately after completing the config (press ctrl-c a couple of times), then go to control panel/admin tools/services and start the service.