The two black lines in the 4 lines is COM, the yellow is +12VDC(pin 1) and the red is +5VDC.
There is no problem in using them as your second PCI power cable to S3 blades.
The double PCI power connectors on a single PCI cable will not serve the purpose.
For this CX500 power supply connect the PCI power cable(6+2) to each blade.
And if you want to connect all the four PCI power ports, use 2 molex to pci to connect one each blade as secondary.
Using molex as pci-e cables is a great way to get melted wires.
Also I don't think there is anything wrong with buying a PSU without an extra 25% safety margin.