The 6700K can max 16 lanes (x16 for single GPU, two x8 for dual SLI or one x8 + two x4's), with the Z170 chipset providing an additional 4 (which can be utilized as x1, x2 or x4 - or a combination of)
With a single GPU, you can run x16 (or SLI at two x8) from the CPU with the NVME drive x4 provided by the chipset.
Currently, you are using x16 for the GPU
You won't interfere with your GPU by populating with an NVME drive.
As an example, if you populated the x1 slot with a network card, it would impact the bandwidth available to the NVME. Your GPU would still be x16 but to provide the x1 for a network card, your NVME would drop from x4 to x2.