some boards will run the pci-e @8x if you use both slots, but it depends on the board. it should be in your manual.
but with that said, current cards don't even use pci-e 3.0 to its maximum so you should be safe.
it's like worrying that the speed limit has been reduced from 500kph down to 300kph, all the while most cars barely reach 200.
i wouldn't worry about it? what is your gpu?
i have a 670 running at 2.0 (because i have an old but trusty 2500k)