Welcome to Motherboards.org.
There is a 'standard' for USB connections.. as noted in this link.. http://pinouts.ws/usb-pinout.html
But some manufacturers still do not adhere to the designated wire color, although the wire function is following the standard.
Most headers are 10 pin type, with one pin missing as a 'key'. The owner's manual for your motherboard should have a diagram of how the pins are configured. Typically only two schemes.. parallel or opposing. But if in doubt about the pin function, remove power from the system.. and use a digital ohmmeter to check which pins are "ground" polarity, to a bare chassis point. Should be a near-zero reading.
For dual headers, you need only one shield connection, but the two "ground" or "return" leads are important.
If you have problems with only one USB port working at a time, check the BIOS pages for USB settings.. and ensure the correct driver is installed. The driver disk that came with the motherboard has the proper drivers. Again, consult the owner's manual.
F@H.. to solve mankind's maladies.. in our lifetimes!