Your qualified dividends (QD) are added to your other income and included in both your total income and Adjusted Gross Income. The special tax treatment for qualified dividends is not an exclusion from your income.
Among your work sheets, you will have a "Qualified Dividends and Capital Gains Worksheet" (abbreviated "Qual Div/Cap Gn" on the forms list) showing the tax calculation. That's where your QD are taxed at 0% or 15%. For more complicated returns it will be the "Schedule D Tax Worksheet" (abbreviated "Schedule D Tax").