In the HSA interview (Federal->Deductions & Credits->Medical->HSA, MSA Contributions), navigate to the screen that is titled "Let's enter your HSA contributions" (see screen shot below).
On the second line where it reads "personal contributions", enter your after-tax HSA contributions here. This number will be reported on line 12 on Schedule 1 (1040) as an adjustment to gross income.
Note that since you included the HSA contributions in Wages on your W-2, this is an after-tax contribution.
[Edited 4/2/2020 11:33 am CDT - updated for 2019]
