Which expansion slot to use?
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Solved by Vitalius,
2 for the Xonar
3 or 4 for the GTX 780. The difference between PCI-e 2.0 x16 and 3.0 x16 is negligible. You literally wouldn't notice it.
It's not different in a way that will harm your performance (though it could be different).
For how it could be different:
In motherboards with lots of PCI-e 3.0 lanes, there are multiple chipsets that handle them all. If yours has more than 1 chipset, (what is called a PLX chipset), it will just change which chipset handles the traffic from the card.
But that shouldn't degrade performance in any way. Unless your chipset is faulty, but then that'd be a motherboard problem and you should RMA.
I don't know the limitations on the default Z87 chipset, so I don't know if you have a PLX chipset, but you may.
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