You need to use the command line version of Folding@Home for my instructions to work.
Make a folder called Folding
Stick a copy of the Folding@Home client(OSX-3.25) in it.
cd to that folder in Terminal and run the client.
Configure all your info and in the advanced area change the machine number to 2.
Your first client has a machine number of 1, Your second has a machine number of 2.
Then you can run them both at once.