Some folks may suggest you use SetiDriver; personally, I use a mixture of SetiQueue and SetiSpy.
But since your question seems geared to running SETI as a service, the only things I can think of would be have to each client in it's own directory, and then as part of the parameters for executing the client, you'd specify which cpu to run it on. On my dual-cpu boxes, I have the cmd-line parameters something like:
seti1.exe -verbose -cpu 1 -proxy 192.168.1.40:5517
Where seti1.exe is the Seti Client, the "-verbose" echos output back to the screen, the "-cpu 1" specifies which cpu to run on, and the "-proxy 192.168.1.40:5517" points to the local SetiQueue that I have setup in my house.
So on my 2nd cpu, I'd simply change the parameters to reflect "-cpu 2"; since I use SetiSpy to track my local progress, I don't bother to use the "-verbose" parameter, and if you're going to be running Seti as a service anyway, you probably wouldn't want that parameter anyway.
Hope this helps!