I have an Asus X99 Deluxe 3.1. In the picture, the red is what I have in the pc already running perfectly. I wanted to add another NVME drive in the blue box on the picture. When I do it Forces the main GPU in slot 1 to run at 8x while it leaves the 2nd GPU at x16. I would like to know how exactly this should work. This is the first time I am loading up PCIe lanes this much on this build. So just to recap what I am trying to do. I have Main GPU in PCIEX16_1 running at x16, 2nd GPU in PCIEX16_2 running at x16, 10Gbit Nic in PCIEX16_5 running at x4, and NVME in m.2 slot rightfully running at x4. I know PCIEX16_5 is connected with the m.2 slot and you can change the lanes used in the bios which is what I had to do to add the m.2 NVME. In the manual, it says I can change the bandwidth of PCIEX16_3 in the Bios. I can't change it in the bios nor can I change any other options other than the generation of PCI-E. I am trying to figure out how the rest of the PCI-E lanes are distributed. I just want to have it take x8 lanes away from the PCIEX16_3 and not the PCIEX16_1 so that my 2080 super can use all 16 lanes while my Titan X can get away with 8 lanes. If anyone knows any more info it would be greatly appreciated. I plan on upgrading to the next-gen x platform so soon I won't have to worry about it. but till then I just want to run one more NVME without sacrificing lanes to my Main GPU. Thanks in advance.
 

That is an option. I just wanted to try all before I have to drain this loop just for an NVME. I just was confused that it would keep the x16 on the 3pcie16 slot over the 1st slot. I can normally drain one side due to my GPUs being higher than most of the loop and draining just enough to pull tubes off and swap the GPUs around. I will probably try it in a few weeks. I just got most of the air out of my loop and that is very difficult to do with this size of a loop. 

Cool GTX
Looks like your stuck
 
If I understand which MB your using .... looks like your not able to do what you want
 

 
Manual Asus X99 Deluxe 3.1
 
 
 
 

Well I was led to believe that it will always divert most lanes to the first PCIe slot. The thing that confuses me is that it puts the first slot to 8 and the 3rd PCIe slot to 16. I feel as if that should have been the opposite. I will maybe switch the two GPUs around to get the lanes split the way I want it.