PCIE Lane Difference

[lilusman77]

Here are my specs mostly:
MSI x99a Godlike Carbon Motherboard
Intel I7 5820K CPU @ 4.0Ghz
EVGA GTX 1080 SC Graphics Card
32 (8x4) DDR4 RAM Memory

Because I have a large Noctua NH15 CPU cooler I I can not put my graphics card in PCIE slot 1. I have it in slot 2. I think with my 6 core processor 5820k only slot 1 will give me 16 lanes. When in GPU-Z it says that it is running on 8 lanes but the graphics card is capable of running on 16. When I go in the MSI Bios 5 and explore my hardware it says PCIE slot 2 and PCIE slot 3 are being used by and NVIDIA graphic card 8 lanes each but I only have the one card plugged in to slot 2.
1. I would greatly appreciate it if someone smarter than me could look at the manual for this motherboard and tell me where is the best place to put the card and if Im really running on 8 or 16 lanes.
2. If I should be on 16 in slot 2 is there a setting or something I need to change to get gpuz to recogonize all 16 lanes?
2. And I know this question has been asked a hundred times or more but will 8 lanes instead of 16 lanes really matter.
We mostly game at 4k when not recording in obs and 2k when recording in obs. I have called MSI about this matter and one person will tell me that it should show 16 lanes and the other one says 8. (not impressed with them btw)

Here is a link to the motherboard manual:

https://us.msi.com/Motherboard/support/X99A-GODLIKE-GAMING-CARBON#down-manual

The PCIe table is found on page 36 of the manual. For 1 way 28 lanes it says 3.0 16lanes on pcie 1 but on lanes 2-5 it just has a line through it so I didn't know what the lines mean.
Thank y'all in advance for your help.

 

[siles2004]

With a 5820K the three big slots run x8 x8 x4
With a 5930K the three big slots run x16 x16 x8.

This is on a x99 Asrock Extreme.

On yours it will be x8 x8 x4 x4 x4.

What might help is to disable the PCIe slots in bios, only let the one active you actually use.

The Mobo is slight overkill for the 5820k

 

[lilusman77]

yeah I know it is overkill for that cpu. actually had a different x99a board but it died and got this one on sell. hopefully I can upgrade my cpu and monitor some day get the full benefit of the board and graphics card.