I have an Asus P5E board...currently the only slot I have for x16 is the lower one (For the 3780X2 dual slot to clear). Now...can I install my card in the lower slot and not have any performance degradation? I'm thinking I'll be fine...but always helps to have other opinions. I can't shuffle any slots around because of some studio hardware using all the x1 slots. The only exception to the rule would be removing the FX sound card from the upper x1 slot and relocating the studio card from under the upper x16 slot to it's location to provide room for the dual slot config on the that x16 slot. This would only happen if I knew that the SPDIF and/or Optical out would still output audio if the card was removed. Sounds confusing...but just really want to know if the lower x16 will be fine...might have to play with some IRQ's but hope it's fine. Any help would be greatly appreciated
I don't know the P5E board well, but is it a P35 chipset? If so, the second PCIe x16 slot is usually only x8 electrical, meaning it's a x16 slot but will only run at x8. You will loose some performance on that slot if this is the case. On average, a single GPU gfx card might loose about ~10-15%, but I don't know how much a dual GPU card will loose.
UPDATE: Ok, so I decided to look it up. Quote from xbitlabs,
So, Asus P5E is a mainboard based on the new Intel X38 chipset and supporting DDR2 SDRAM. As a result, it is compatible with all LGA775 processors including the Penryn CPUs and features two fully-fledged PCI Express 2.0 x16 slots.
In this case, both slots are full x16 electrical, you shouldn't loose any performance at all.