W2 and 1099 NEC filled together. How do I pay for 1099-NEC Taxes or will they be deducted automatically from the tax refund?

Taxes on 1099-NEC will be "deducted automatically" when the return is done.

I think you may be wondering about the self-employment taxes associated with income reported on a form 1099-NEC. If so, it was reported on your form 1040 individual federal income tax return. As such, the refund or taxes due as reported on your form 1040 will include the self-employment tax along with income taxes associated with your form 1099-NEC. So, nothing additional will be subtracted from your refund.