If it's a 2016 W-2, it will need to be filed on your 2016 return. If you have already filed the return with adding it, you just need to wait until the IRS has accepted your return and you have received the refund. Once you get the refund, then you will need to file an amended return to add the additional W-2 to your return.
After you have received your refund, you can go here and get instructions https://ttlc.intuit.com/questions/3061514 for amending that return.
And this link will give you the steps on where to enter your W-2 when amending that return https://ttlc.intuit.com/questions/2866494
NOTE: The IRS gets a copy of each one of your W-2's and they will check to see if you report them all. If you do not file both, you will have to amend your return to add them.