You should file only one tax return a year (1040, 1040A, or 1040EZ), no matter how many jobs or W-2s or 1099-MISCs or other forms that you receive.
Yes, people say "I filed my W-2", but that is incorrect - you filed your 2017 tax return, and you should include all of your W-2s that you received for that year.
This is why you need to wait to make sure that you have all your forms before proceeding with your tax return.
Did you include both W-2s on the tax return you just filed for 2017? Then you are done and the refund covered everything.
But if you filed your return with only one W-2, you need to amend your return to add the other W-2. And note that the IRS receives copies of every W-2, 1099-MISC, and other forms that you receive - so if you leave a form off, they will be aure to write you about it and possibly charge you penalties and interest for not reporting this income.
For information on how to amend your return, please see https://ttlc.intuit.com/replies/3288565
