one and two for 16x if you use one and three it will be 16x 8x
It would only run the 3rd slot at x8 if there are 3 cards, then it would run 16x 8x 8x iirc, you can use slots 1 2 and 3 in any combination and still get 16x on both.
I could be wrong but if i remember right it actually recommends 1 and 3 for dual cards in the manual (BTW i dont just read random mobo manuals, a friend of my cousin was asking about gpu setups on that board bout a month ago
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@ OP you can use 1 and 3 no problem.