Hello ialam,

If you're adding an employee HSA contribution (a deduction item). Please follow the steps below:

1. Go to the Workers tab and select Employees.
2. Choose the employee and click on the pencil icon for Pay. 
3. Click on the Add deductions link.
4. Choose Deduction/Contribution. 
5. Choose HSA plans from the Deduction/contribution type drop-down menu.
6. Choose either Pretax HSA or Taxable HSA from the Type drop-down.
7. Enter the description and choose % of gross pay from the Amount per pay period. 
8. Click on OK.

QuickBooks will automatically calculate the HSA deduction on the employee's payroll. Also, these deductions will be reported in the box 12 of W-2 forms. But, this is excluded from federal wages (SS & Medicare) and most state wages. 

For more details, please check out this article: Set up Health Savings Account (HSA) Plans.

Otherwise, you'll need to add it as an additional pay item. This will be reported in the employee's total wages. To learn more about it, please see this article: S-Corp Owners Health Insurance.

We'll be glad to help if you need anything else.