Core 2 Duo

I just built a new Core 2 Duo E6600 computer and would like to fold on both of my cores, how do I do this?

Can I put the folding client in different directories and run one instance from each?

I generally create a FAH directory and FAH1 and FAH2 subdirectories. Download the FAH504-Console.exe from stanford, put a copy in each subdirectory, run it from each directory with the -config flag being sure to give the instance in FAH1 machine ID 1 and the instance in FAH2 machine ID 2. Personally I'd run FAH as a service(s) but others opinions vary for personal tastes and use patterns.
Don't use the GUI (5.03). You can only run one instance of it per machine anyway.