Beginner, Confused as to how to solder a "Y Split" Molex Connector to a USB
On such a Molex connector, yellow is for +12VDC and red for +5VDC. Both black wires are ground (GND) or 0V, the return path. Either of the black wires will do... although, by convention, you might want to use the black wire that is close to the coloured cable for the power signal return path.

The yellow wire is useless for you since USB only has +5V on its (typically) red wire. you can then keep only the red wire and one of the black ones. Be sure to pair the wires that you keep with the fan's on the other connector.

You can safely chop the data wires (+ and -) off the USB cable. Better insulate them to prevent accidental shorting or contact with the power wires.