I am using both of the supplementary power supplies (6 pin and 8 pin) but on the 6 pin, i only have 1 molex connected (out of 2). Does that matter ? And if so, what's the risk ? The GPU is an EVGA GTX 760 Superclocked.
You should use both. What power supply do you have? If it's powerful enough for the card it should have the proper connecters.
I have a 550 Watt power supply which is enough for my GTX 760. Though, there are 2 molex for the 6 pin plug and i only had 1 molex connected to the power supply.