Check your Mobo Manual for the placement of the PCIe cards. It will tell you exactly which slots are linked to which ones, thus by adding anything in 2 linked slots will reduce the speed of the other slot.
You can choose another slot if available and not linked to the one that holds the GPU if you feel like it.
Although the difference in functioning at 8X or 16X is not going to effect game play for you since it's not that obviously visible on the Monitor.
Though you will see the difference in Synthetic Benchmarks. Usage wise it's not going to e a problem, unless, conflicting hardware is used.