Which CPU do you have? PCI-E 3.0 is only available on Core i5 and i7 3xxx CPUs. Sandy Bridge CPUs, and Ivy Bridge based i3s, Pentiums and Celerons don't have PCI-E 3.0 support.
Either way, it won't make any real difference. The 660Ti is not powerful enough to fully saturate PCI-E 2.0 x16. In fact, no single GPU card in existence right now can fully saturate PCI-E 2.0 You will see no performance difference with PCI-E 3.0