Let me clarify things out, vvicky72.

As mentioned in this thread, you won't select the company HSA contribution for shareholder-employees who own 2% or more of an S corporation. This benefit is taxable at the federal level and in some states.

You need to set up the S-Corp pay type on your employee and enter the amount from there. This will be reported on the W-2: Box 1 and $ amount in box 14 with “S CORP OWNER”.

Let me show you how:

1. Go to Workers from the left navigation bar, then choose Employees.
2. Click the employee to open the profile.
   
3. Go to the Employee details tab, then click the edit (pencil) icon beside Pay.
   
4. Choose How much do you pay, then click + Add additional pay types.
   
5. Click Even more ways to pay.
6. Mark S-Corp Owners Health Insurance, and enter the amount.
7. Select Done.
   

After that, you can then run payroll that includes the S-Corp contributions.

I've added this article for additional information: Set up and record S-Corp health insurance. it provides three ways to do enter this pay type in QuickBooks Online.

Don't hesitate to get in touch with me here anytime you need a helping hand. I always have your back.