http://www.overclockers.com.au/folding/service-nt2000xp.htm
The page above is not 100% correct when used with FAH3. Make sure you change the file names as appropriate for use with the FAH3 client.
Also, as Coug mentioned, the first time you run the console client for each installation (in separate folders), run it manually rather than as a serivce. Make sure you go into the Advanced settings during set-up and set a machine id 1 for one process and machine id 2 for the other install. Your settings are saved in the config file in the directory (you will see it).
That is it, it is really very simple and stays out of your way when you run it as a service. You can still look at the log file to monitor work progress.
BTW: The -local switch doesn't work now and is replaced with the machine ID thingy above. All you need is the console client...the other stuff is fluff.
Clocker