Depending on your graphics card and motherboard, some of the PCI-e slots on your motherboard will be specifically meant for use with your primary graphics card. This is because not all slots are created equal, with some slots offering the full x16 lanes, while others will have only x8 lanes, or even just x4 lanes.
The top slot on your motherboard will typically be the best place to mount your graphics card, as this is most often the slot that runs at the full 16x speed (with the full x16 lanes), but to make sure, it's worth checking your motherboard's manual.
Should you need, or for various reasons decide to mount your graphics card in the second or third PCI-e slot on your motherboard and these only run at 8x or even 4x speeds, they will still work, but performance can be lower than in a full speed slot.
It's worth noting that the PCIe standard is backwards compatible, so you can, for instance, use a PCI-e 4.0 graphics card in a PCI-e 3.0 slot without issue, although you will see a small performance hit.
