Create two folders
mkdir \distribfold1
mkdir \distribfold2
extract the client into each folder
make sure you put handle.txt in each folder
make sure autoupdate.cfg is in each folder

edit foldit.bat in each folder, look for the line that looks like this
.\foldtrajlite -f protein -n native

change it to this (windows OS - need 256mb ram)
.\foldtrajlite -f protein -n native -rt -qt

You should also edit foldit.bat in each folder to add DFPTEMP variable to point the swapfiles someplace different from each other.

for example...
set DFPTEMP=\distribfold1\TEMP (in the first case)
set DFPTEMP=\distribfold2\TEMP (in the second case)

then
mkdir \distribfold1\TEMP
mkdir \distribfold2\TEMP

This prevents each client from stepping on each others temp scratch files, which has happened before when using duals.

open a cmd prompt
Then
cd \distribfold1
foldit

open a cmd prompt
cd \distribfold2
foldit

There is no way that I know of to dedicate each client to a different processor.