You don't need to bother with shorting the two black cables (GND), but you need to route BOTH of them to both ends.
The reason is simple: they ARE SHORTED in PSU, anyway. So short the cables elsewhere don't harm your computer in any form.
Using two mini-molex (intended for connection of floppy drives) and solding both to the PSU connector makes the voltage drop-out a minor problem and free the middle lay (on multilayer PCBs) current.
