Do I file an injured/innocent spouse claim after I file this years taxes since I just received notice in 2010?

My spouse filed our taxes last year and falied to enter a w2 so I got notice that he/we owe. We have been seperated for over 8 months but we have decided to go ahead and file jointly to take care of this debt we owe to the irs, I am going to file the injured/innocent spouse claim but I would like to know if I should wait until they inform us they have taken our federal refund for this year or go ahead and file it when we do our taxes?