can you provide more info what you mean. Schedule D will show short term and long term cap gains separately and then the combined total which goes to the 1040.
tax calculation is not done on tax tables based on the taxable income shown on your 1040 which combines all income - the calculation is done on the "Qualified Dividends and Capital Gain Tax Worksheet" which separates the LTCG and Qualified Divs for tax calculation at 0/15/20% and the remainder is taxed using the tax tables.
