Last year I filed jointly not meaning to because only reported my income. Than my wife filed separate a few months later. This year we found this out while trying to file electronically and wouldn't let us. We need to file amendment now and I wanted fix mine because I should have done separate. But on the 1040X it says cannot change to separate after due date which I assume was last April. Now do I fill out 2 amendments for me and wife or just 1? Because me and wife only reported what we did on each of ours.

You are STUCK with filing JOINTLY for 2011, because, once the 15 April 2012 filing date passed, it became an IRREVOCABLE decision.

You Do need to amend the 2011 return to add her income to the return, but you cannot change the filing status to Married Filing Separately.

Thank you. So just fill out the 1040X right and add my wife's income? All the other stuff on the form doesn't need to be filled out like the tax liability, payments, or refund amount you owe? And on exemptions if I didn't put my wife on the jointly just add her right in the net change column?

No, when you add her income, the tax liability changes, and I assume she had money withheld on her W-2, so the payment information changes as well.

May I recommend that you get professional help? Any competent local tax pro can do the amendment.