it may not matter.. but when I install dual smp's. I run the install twice for each dir... nothing is copied from one dir to the other....
then run both install.bat's and both .exe -flags with adv config ques answered the first launch of both clients.
then restart to make the "disable affinity lock" take in the client, since it says it needs a client restart to make the adv config ques stick....

but we all know there's more than one way to skin a cat, and you'll probably find zero ways in the fah faq