You don't need to explain what you paid. The $2,000 that you paid with your original tax return should be on line 16 of Form 1040-X, which includes "tax paid with original return." Line 18 should be blank. You did not have an overpayment on your original return, you had an amount due. You don't "input" anything on line 21. Line 21 has to be calculated as specified on the form.
If you use TurboTax to prepare your 1040-X it will fill in the form for you.
How do I amend my federal tax return for a prior year?
