On line 3 of the QDCGT worksheet, as you say, you enter the smaller of your long-term gains and total gains. Assuming you did not have a loss in either category, your long-term gains will be less than both long- and short-term combined, so you will enter long-term gains here. On line 7 of this worksheet, you effectively subtract your long-term gains from your taxable income, leaving your short-term gains lumped with the rest of your ordinary income on Line 7. Most of the worksheet then computes your tax on the long-term gains, but on Line 24 you compute the tax on Line 7, which, as mentioned, includes your short-term gains.
Thus, this worksheet lumps your short-term gains with the rest of your income. Your short-term gains do not get the preferential tax treatment which is encoded in line 8-23 of the QDCGT worksheet. It is not easy to see this because the logic of those lines on the worksheet is rather opaque. The rough summary is that, since your long-term gains alone are always smaller than your total income (including short-term gains), the various lines which tell you to enter "the smaller of X or Y" result in you entering your long-term gains (or portions of them falling into various brackets), on which the preferential tax is then computed.
So when you went through that worksheet, you were treating the two separately, you just didn't realize it. The amounts on Lines 20 and 23 are your capital gains taxes, and whatever amount you had on Line 11 was taxed at 0% (as mentioned on the worksheet). If you had had no long-term gains, all of your income would have remained on Line 7 and been subject to ordinary-income rates as computed at Line 24. If you use the tax table on your total taxable income, you should get a higher number than you wind up with on the final line of the QDCGT worksheet.
