You pay taxes on your total income after deductions and credits. The self-employment income is going to result in self-employment taxes but the net income is also taxable income for regular income taxes. The rate that is applied depends on all of the income on the return. Thus, it's not possible to accurately calculate the estimated tax payments required if you don't include all of your income.
Likewise, this is why you also include all of your available deductions and credits as those items could reduce the taxable income amounts and thus result in less tax due. But, you will also see a screen in that section where you will enter your Federal income tax withholding amounts for your W2 wages - make sure you enter it to get an accurate result of the taxes already paid.