The manual states that when the M.2_1 socket (the one above the graphics card slot) is being used (whether in SATA or PCIe mode) the SATA6G ports 5/6 (the ones nearest your RAM) will be disabled.
If you use the other M.2 socket, your graphics card will run in x8 mode.
If your OS SSD is running in port 5 or 6, remove the NVMe, switch the SSD cable to another port and reboot. Make sure it's all working before shutting down and installing the NVMe again.