And the W2 accounts for all HSA contriubutions done through your employer, nothing else gets entered anywhere about HSA contributions unless the TP made them out of pocket on their own.

You will still have to use Form 8889 to show that the taxpayer was eligible to deduct the $2000 or it will end up being added to the T/P''s income.

The employee's W2 should show this as contribution to an HSA in box 12 of Form W-2 with code W. That should trigger the program to put it as Pre-tax, already. The employee does not also get a deduction, since it was pre-tax.