Once the second card is inserted into the second PCI-E slot the lanes will be automatically split up depending upon which motherboard chipset and CPU is being used. In your case the automatic split is X8/X8. You don't have any control over this.
The difference between PCI-E X16 3.0 @ X16 and PCI-E X16 3.0 @ X8 is only 1% or less. You wouldn't even notice it.