If you had entered the additional W-2 with your original return, then your refund would not have been as high. Therefore, when you prepare your amended return you must pay the difference in that refund amount. The best way to see why you owe more is by looking at Form 1040X. If you look at line 5 of Form 1040X you can see if the additional W-2 caused you to have more taxable income. If column C is higher than column A, then it did.
