PCIe slot configuration advice

The PCIe slot "limitations" for graphics cards on Intel platforms are all based upon the number of PCIe 3.0 lanes provided by the CPU. For every mainstream processor generation since Ivy Bridge and including Skylake, that is 16 PCIe 3.0 lanes.

From that amount they are divided up among the PCIe 3.0 x16 slots. The Skylake platform, or really the Z170 chipset, is different than all previous Intel chipsets. It also has PCIe 3.0 lanes but they are used for SATA IO, and for the M.2 slots with PCIe SSDs. That means that PCIe SSDs will not necessarily use the PCIe lanes provided by the CPU, so no lanes are lost for video card use when PCIe SSDs are used.

The PCIe lane allocation for the video card slots, given 16 PCIe 3.0 lanes from the CPU is:

4 x PCI Express 3.0 x16 Slots with 16 PCIe 3.0 Lanes shared between slots PCIE2, PCIE4, and PCIE6.

A single video card will operate at x16 in slot PCIE2.

Dual video cards will each operate at x8 in slots PCIE2 and PCIE4. Slot PCIE4 is an x8 slot maximum.

Three video cards will operate at x8 in slot PCIE2, at x4 in slot PCIE4, and x4 in slot PCIE6. Slot PCIE6 is an x4 slot maximum.

Slot PCIE3 is an x4 lane slot, but is connected to the Z170 chipset's PCIe 3.0 lanes. That slot is meant for use with PCIe SSDs like the Intel 750, or other kinds of PCIe cards.

The Ultra M.2 slots are mounted lower than all the PCIe slots, and neither interfere with the others physically. M.2 SSDs that are covered by a video card will not get much air circulation and tend to run hotter.