The above is correct. You must read your manual carefully. It clearly says that if you are going to run two (2) cards in SLI then you should run them in slot one (the red slot nearest the CPU) and slot 2b (the black slot between the middle two red slots).
It maybe that you can use others, but if you follow that configuration, you will be running each of the two cards X8 PCIe 3.0; and that is equivalent to X16 PCIe 2.0. Further, the board will run both slots "natively" meaning the PLX chip will not be used. This is the most efficient method to use two cards in SLI on the Maximus V Extreme.
Just finishing TJ 11 WC.. trying to control cooling via total PWM
Asus Max V Extreme
Intel 3770K
Corsair 16gig Platinum 1866
2 X GTX 690 (EVGA) with aftermarket EVGA water blocks and backplates
Samsung 830 Series 512GB + 3 WD mechanical HD's
Swiftech Apogee Drive II
Swiftech MCP35X2
Alphacool NexXxos UT60's quad, triple and single 120's
Rad fans 11 x NF-F12 PWM
Corsair 1200i PSU
Swiftech Maelstrom
AFT Pro-57U card reader