Nah! the Blue PCI-Ex16 slot runs @ full 16 lanes while the 2nd PCI-Ex slot runs at a max of x4, so in a way you can put the GTX card in the 2nd slot (black one) but the card's performance will drop by more, way more than half.
Think of it as an AGP 8x card running at 4x only, putting DDR 400 on a chipset that can handle DDR 333 only.......it would be a waste of performance to put the GTX in the 2nd PCI-Ex slot (black one).
When you put the GTX in the blue PCI-Ex slot, you're still going to be able to use TWO (white) PCI slots (2nd white and last one), unless you're getting a GTX 512. What other PCI cards do you have that you have to use 2 or more? or you just want to have the ability to use 2 or more in the future?