1040-X and Stimulus Payment i

I made a mistake on my 2007 return. On Schedule D I failed to enter the sum of short term capital losses on line 7, although I did the calculations for line 16 correctly. The IRS did the calculation based on line 7 being zero, and increased my taxable income, and thus my taxes. They deducted this amount from the stimulus payment I received. To add insult to injury, I did not notice this until today. So I will have to file a Form 1040-X, along with a revised Schedule D. My question is how to indicate that the IRS already took my overpayment. Do I add it on line 17 of Form 1040-X, as "additional tax paid after it was filed"?