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If your card has an x4 pinout, then it probably needs the additional bandwidth. Plugging it into an x1 slot (if it was possible) would slow down the network traffic. Get a better motherboard with an x4 slot on it so you can use the hardware you want. or find something else that will fit your computer.
Honestly even the 1Gb quad port card I have requires an x4 slot, although I saw some dual-port 2.5Gb x1 cards on ebay. Maybe you could just use two of those?
It doesn't need that kind of bandwidth. 6 gigabit ports cannot saturate pcie gen 3 x1 in terms of bandwidth anyway.
What do I do if the card is PCIe gen 2 x8 though?
Potentially the same thing, assuming PCIe 2 x1 provides enough bandwidth.
Pcie 2.0x1 would have a theoretical max of 4gbit/s so it would probably only handle 3.5 gigabit of connections simultaneously.