Although you specifically said the two ports on the PC board, I suspect you really meant the two USB ports (A and C) on the back of the unit.
Either port can be used for connecting any of the following:
1) an external CD drive for ripping CDs to the internal hard disk, which is faster than using the internal CD mechanism;
2) a USB disk for Importing or Exporting music;
3) WiFi dongle
3) Bluetooth dongle
When connecting an external drive (either CD or disk), USB port A provides somewhat more power for a device that needs it and may not function well on port C.
Now if you're really talking about the internal PC board, I have not looked at it. But I do know that USB port B is used internally for the hard disk. That's why there is no USB port B on the back of the unit. (Or, on older units, that's why it can't be used.)