An amended return can only by filed by mail and you will receive a paper check for any refund due from filing it. The two returns do not crossover, they're processed separately. Nothing you've entered for the amended return will interfere in any way with the original return. All you've done is enter it, it doesn't go anywhere, meaning nothing goes to the IRS,
For an additional W-2, don't forget to also amend any state return you may have already filed.
