I believe my tax lady replaced the W2 numbers from the company with the values they should have been. She then redid the rest of the computations normally with the updated numbers. The letter attached to the amendment explained why the company's W2 numbers were incorrect and why the correct numbers had to be the one she used. Then there is a final document with the difference between what was originally filed and the amendment, giving the expected refund.
The IRS took that number and added interest and sent me a check.
