This is why its SO important not to file until you have ALL your paperwork.
You need to wait for the original return to either be accepted or rejected by IRS. If rejected, you can add the W-2 and refile the return electronically.
If it's accepted, then you need to wait for the refund to be issued, then prepare an amended return, print, sign and mail it in, and wait the 12-16 weeks for them to process it and mail you any additional refund you may be entitled to.
Its possible that the additional W-2 actually reduces your refund, in which case you'll have to pay back any excess refund you received on the original filing along with the amended return when you mail it in. This money is due by April 18th, 2017.