Box 12 of your W-2 includes both the employer and payroll contributions. I would not override the amount reported if it looks correct for the total contributions made to the HSA. Line 9 on Form 8889 should be the same amount as Box 12 Code W on your W-2 and consist of both employer contributions and pre-tax payroll contributions.
The IRS considers employer contributions to include salary reductions through a cafeteria plan.
