I personally have my RAID card in the top PCI-e slot and set the bottom two to 16 X 1 rather than the 8x8 you can pick in the bios, I'm not even using the bottom one.
The V2's at least will run 16x16x1, or 16x8x8.
Part of the reason I picked it up was the layout, so I could cram everything back in here, I looked at a few MOBO's just to get a layout I could use to keep my RAID card, Auzentech, and the Killer NIC in here.
Seems to be working pretty well, even if the GPU is in a lower slot.
Now if I ever can convert my HD4870x2 back to stock and get it running right again I'll be a happy camper, wish I'd never put that accelero on there. It actually ran fine awhile, can't blame Artic Cooling, I started messing around more and fudged it up myself, been having a few probs trying to get it back to stock, just to fit it in the bottom again, heh.
Oh well, thats off subject I guess, if nothing else I'll use this 260 for now which works ok and switch to a 5XXX in the future
Other than that, and the fact I'm new to it, I've had relatively few problems. Not problems even, just was some of my reasons for picking it.