How should I file our taxes?

My husband and I usually file married filing jointly. He's usually the bread maker. This year I worked for about 2 months with a total income of $1000 and some change. He received a notice that his taxes would be taken due to child support. He's been out of work a majority of the year but earned more. We usually get EIC and use it on our kids for things they'll need through out the year. If our taxes are taken, we won't get any of that for them. My question is should I file separately or file injured spouse and will I even qualify for EIC? I'm usually pretty good about figuring our taxes out but this is a new situation for me.