amp power up fine?
are the 6x9s powered off the amp and playing ok?
check connections from sub to amp, making sure wired up correctly.
If all wiring is ok, and 6x9s are working ok, could be faulty sub.
Oh and try swapping the connections from the 6x9s and the sub, so the sub is running from where the 6x9s where connected, to make sure its not the connections off the amp.
Oh and are the amps fuses ok in it - has 2 external fuses being a 4 channel?