Generally you want to use both of the molex connectors, the reason is that there is a huge amount of power being sent to the video card over these wires, and the wires are small. Spreading out the power over multiple wires will ensure things like the wires melting won't happen. It's best if the two molex connectors you use are are on different wires coming from the power supply.
Even better would be to replace the PSU with a supply that's designed for modern computers.