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If the GPU is using legacy interrupts for some reason, it may be suffering from high latency while the CPU is busy handling other interrupt handlers for that IRQ.
Your motherboard's user manual specifies that the PCIE x16_1 slot (the top one) shares IRQ assignments with the internal graphics, HD Audio, USB 2.0 (EHCI), and PCI 2 slot.
Modern motherboards ...
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There should be no issues running your GPU in the second slot. That said, it's important to note that running any GPU in that means it only receives 8 PCIe lanes of bandwidth, instead of the full 16 it would get in the primary slot. However, since your GTX 960 is a relatively old and slow card, it's unlikely that having access to only half the lanes will ...
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It's best to do the following:
Add the non-free section of the Debian repository to the list of package sources to APT. See this.
Run # apt update
Now you have the nvidia-driver package available—it depends on a number of other packages which provide nVidia-produced "binary blob" proprietary driver.
The upside of using it over whatever you have ...
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Graphics cards have never been able to "appear as one" device.
For many years we have had SLI and its AMD counterpart Crossfire which used two or more graphics cards to render a single scene, but this requires a bit of hardware and a lot of software support.
In essence the software gives both cards an exactly identical set of data, runs the graphics card ...
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Can't speak to gaming, but 3 x 4K@60hz works fine with my 1060 6GB for programming. No different than a single screen.
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