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.
Take a second look, Its auxiliary for the second. I wonder whats wrong with it.
My Sapphire GPUs even came with this kind of molex->PCI-E for the second power slot.
I'm using it since last 4 months for ASICs and earlier for GPUs. They will not even get hot.
Wonder how to add extra safety margin by buying a new PSU.
No PSU will give enough PCI Slots enough to connect 4 ports of S3.