It should go in only one way, the right way, since USB has been standardized now.
I always check the pinout with the case manual if applicable and the motherboard manual. You could burn out the motherboard with the wrong connection as said above.
If the bracket came with the motherboard, your only worry is connecting it to the wrong header. Make sure you do not connect it to the firewire port.
Connecting it to the firewire port would burn out the motherboard.