Plug the GPU card into PCIE_X16_1 for best results.
Plug the M.2 card into any of PCIE_X8_2, PCIE_X4_1, PCIE_X16/X8_3, or PCIE_X8_4 - it won't fit into PCIE_X1_1 anyways.
The R5E design suggests PCIE_X8_4 is the preferred location, but I would recommend PCIE_X16/X8_3 as the "best" available slot if one GPU card and nothing else is plugged in.
If a second GPU card is installed (in PCIE_X16/X8_3, of course) the "best" slot for the M.2 is again PCIE_X8_4 - but, if chipset/PCH bandwidth isn't already being saturated with SATA/USB devices, and if airflow and space around the GPU cards is adequate, then I would actually plug it into PCIE_X8_2 to keep PCIe 3.0 bandwidth dedicated entirely to CPU-GPU traffic. There is a difference (in terms of real fps and benchmark performances), but it is generally small.
Your BIOS may impose additional limits on M.2-compatible slot placements.
RAIDs and boot/system drive configurations are sometimes "lost" (technically they become incompatible or may need their partitions and file systems rebuilt) after UEFI/BIOS updates. Best to always backup before updating firmware, be prepared to fully reinstall/restore your OS/system afterwards if necessary.
"All opinions are not equal. Some are a very great deal more robust, sophisticated and well supported in logic and argument than others." - Douglas Adams
[/Korth]