No amount contributed through your employer is to be included on Form 8889 line 2 as a personal contribution. All amounts deposited by your employer whether taken from your paycheck or not are to be included on line 9 because they were not included in your wages on line 1 of your W-2.
Personal contributions that are includible on line 2 are only those that you deposited into the HSA yourself without involving your employer. If you made no such deposits, leave blank the amount when asked if you made any personal contributions.
