You should probably give them a call to see if you are still current, when Centrelink receives the information from the ATO they may automatically pay you what your are owed for the 08/09 financial year. Or you may have to lodge a lump sum claim form (is not too detailed so don't worry).

You may want to discuss the option of the being made current for FTB but received 0 rate, then you won't have to worry about lump sum claims from now on you will just automatically get paid when your tax information for both you and your partner come through.