I also wanted to know if I could put a PCI Express x16 graphics card into the second slot on ASUS P6T Deluxe V2. If you have a x8 PCI Express card then it really doesn't matter but a x16 PCIe card needs full x16 lanes (well, in theory). Basically all motherboard manuals I have read suggest we put a single card in the primary PCIe x16 connector for optimum performance.
I have put mine in the second (PCIe_2) connector and GPU-Z and other similar tools report that it is running at x16, so that is cool. But since PCIe_2 shares bandwidth with PCIe_3 I believe it also shares it with other PCIe slots (with PCIe x1 and PCIe x4). I don't have them, populated but still, I'd rather know to be sure it really runs at it's max capability. PCIe_1 is supposedly the only slot which always has x16 lanes dedicated.
Intel X58 supports 36 PCIe lanes. 16 are dedicated to the primary PCIe x16 slot so you're left with 20 lanes. Now if you put a PCIe x1 card in PCIe_3 slot and PCIe x4 card into PCIe x4 slot, you're left with 15 lanes which is what PCIe_2 will get. That's probably enough even for most higher class cards at the moment. But since you probably don't use all PCIe slots, the PCIe_2 will get its 16 lanes.
So I think they wrote that it the manual just to be on the safe side. In real world putting a card in the second PCIe slot will be just as good in the majority of all cases.
So that's my theory.
If I'm wrong and someone can correct me, please do so! I want to learn, too.