I filed as married jointly but my husband filed married separate, what do we need to do in order to ensure that the IRS knows we want to file married joint

[ryan-here-to-help]

The answer depends on which person filed the tax return first. 

Scenario 1:

If the wife filed the return first as married filed jointly, the husbands return which was filed AFTER will get rejected. In this scenario no additional action should be required as your return will be filed Married Filed Jointly.  

Scenario 2:

If the husband filed first as married filed separately, and then the wife filed as Married Filed Jointly both returns will get rejected. When that happens you should only file the return for married filed jointly.