First: If you make employee contributions through payroll, they are only reported on your W-2, both employee and employer are only on your W-2. When you are asked later in the program if you made extra contributions, ONLY enter any extra out of pocket contributions you made directly to the bank, do not enter your voluntary payroll contributions again.
Second, you must indicate in the program that you had qualifying HDHP coverage for the entire year, or you must check boxes for each month as to whether you were covered by self HDHP, family HDHP, or other coverage. Your eligibility depends on your coverage, which your HSA bank does not know.
