If you wanted to file a joint return then everything was supposed to be on ONE return for both spouses--not a "his and hers" set of returns. So you messed up. If your return is accepted then you have to wait for it to be fully processed and then amend it to file it as a joint return correctly. You cannot change anything while it is pending. If you get lucky and the IRS rejects it, you can fix it and re-submit it. Post back for further help.