You only need to amend one return from married filing separately to married filing jointly. After you amend one return, the IRS will ignore the other. You should amend the most complicated return so this way its less work to add the remainder. This article from TurboTax below is very guide at guiding you through the details.
You do not HAVE to amend the prior return before filing this year, but it is generally best to do so because you may have carryover amounts from 2015 to 2016 that need to be accounted for on your return.
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