I don't quite understand how many lanes my system has, or can be used.
4, 16GB dimms
1 PCIe 3.0 x16
1 PCIe 3.0 x8
1 PCIe 3.0 x4
3 PCIe 3.0 x1
2 M.2 slots
6 sata ports.
I have 1 x16 video card installed and 2 M.2 NVME drives, raid 0.
When I install the 2 M.2 PCIe NVME drives, 2 sata ports are no longer useable. (They no longer show up in the board explorer)
Will I be able to add 2 - PCIe x4 NVMe controllers and put 2 more NVME drives? I am assuming this would render the 4 remaing SATA unusable also.
The M.2 Type B/M Sockets include support for both PCIe (NVMe) connection and SATA connection. When you install a NVMe drive, the SATA lane routed to the connector is disabled. If you add a PCIe x4 card that then hosts a NVMe drive, on the other hand, there will not be a SATA lane routed (dedicated) to this card and this none will be lost in the process (i.e. your 4 remaining SATA lanes will remain available).
Your i7-7700 processor has only 16 PCIe lanes and all of these are dedicated to the support of the x16 slot (and presumably your add-in graphics card). The processor then uses the DMI bus to communicate with the chipset (PCH) component. The PCH uses the DMI bus bandwidth to support its internal devices (like the SATA controllers) and to also provide additional PCIe lanes for downstream devices and slots. In some case, additional PCIe lanes are created using one or more PCIe Hubs, which shares the bandwidth of a single PCIe lane across some number of additional PCIe lanes.
Yes, that "Hey, wait a minute..." thought you are having is true; the further downstream you go from the processor, the more saturated the PCIe traffic becomes. When you add that PCIe x4 card to host your extra NVMe drive, this drive is sharing the bandwidth of the DMI bus with the other devices in and connected to the PCH. Add a second card and it is shared even more. Bottom line, these NVMe drives that you add are not going to perform as well as they could.
Hope this explains it (in all its depressing detail),