Sweet mother! I never heard of these, and I did a bit of research on this.

For the curious: PCI-e Switches

...anyway, for the actual answer, I believe that you just set your SimpleMining overclocking section like this:

Core MHz [1165 1165 1165 1165 1165 1165 1165 1165 1165 1165 850 850]

(don't use those numbers, obviously, but the idea is set a number for each card)

You might have to boot into another linux and list your video cards in order to know what order linux finds your video cards...

...that or you can type 0, 1, 2, etc into the console to turn off and on your cards... hahaha... this will not work for all 12, but for the first 10 it will