Should we file married or married but separate or single?
You absolutely cannot file single. In no circumstances. You lose the earned income credit if you file separately. Depending on your combined income you may lose it anyway. You also lose child tax credits if you file mfs. You can do your return married joint and do married separate and see what turns out best. It also depends on what state you are in. If you are in CA it is a community property state. You have to add both your incomes together and divide by 2 if you file separate. Might as well file joint.
