Yea don't put it in the x4 slot. My recommendation is you want better temps. but the DS (Dual Fan) card on top , they like it at the top. then the reference cooler on on the bottom. Thats what i did with my SLI setup. but hopefully i can snatch up a nice kepler card to out perform my setup. or even two cards for a SLI GTX 600 series setup. But nah dude, dont put it on the x4. keep them together for a x8/x8 or x16/x16 setup. x4 just cripples it to the point of its better to have 1 card
The X4 slot just wouldn't allow any card to run at it's full potential.
Temps is one thing to take in consideration.
See if anyone card becomes a bit hot. If it does, try upping the fan speed a little.
The first set up you see is with a Gigabyte board, and you can see there would be a tiny gap, but the second one is with my board, it shows that there will be a PCI slot free between the two PCI-E slots.
Put the DS in the top slot as this card will do most of the work. In an SLI setup, only the first card's RAM is actually used (the card your main monitor is connected to). The only part of the bottom card that is used is the GPU chip for graphics processing as well as the actual CUDA cores, this is a common misconception about SLI - therefore if the bottom card's RAM is inactive less heat will be generated. That being said you probably won't notice a performance difference anyway no matter which card is on the top, just a difference in heat generated. And on a side note, the DS is on sale at overclockers.co.uk and I opted for a second GTX 580 with backplate because I want to be able to stare at it in all its beauty through the side window... I'm OCD and have to have identical cards.