if you make a direct contribution to an HSA (called an 'employee' contribution), you will enter an adjustment to income using the 1099 SA form you receive to document the contribution. - because, you are correct, you are contribution are after tax money.
it is better to have the money withdrawn from your paycheck (a "employer' contribution) because it is deducted from your paycheck PRIOR TO social security and Medicare taxes.)
so you never pay SS and Medicare taxes on contributions via the paycheck, but of course, you have already done so if you make a direct / employee contribution
