The GoFlex Desk for Mac drive comes with two interfaces, USB 2.0 and FireWire 800.
This allows the drive to be optimized for different computers. If the computer has a FireWire 800 interface and an available port that is the preferred interface as it will allow the highest transfer rates. If the computer only has USB (slower, but more popular) you can use that port.
In total there are three connectors on the drive.
The two FireWire 800 connectors allow the drive to be included in a daisy chain. This is where one connector goes to the computer and the other connector goes to another device (like another drive).
You should not have any two connectors on the drive connected to a computer (or multiple computers) at the same time.
Choose to use either: