I filed my taxes with the W2s I received from my employer, but I separately completed and sent Form 843 (https://www.irs.gov/instructions/i843) with proof of my overpayment, and a letter from my employer saying that I overpaid. I owe on my federal taxes this year, but I have not paid yet, as I am waiting for the IRS to confirm the amount that I owe (e.g., subtracting my overpayment on social security).
