I have the exact same issue and our accountant has not found a way to make it work via QBO unless you set the HSA account up like a contractor and do a separate DD. I’m not sure why the responses here are missing the question so blatantly. You have more than explained it thoroughly and there are thousands of customers who want to know why this simple and routine action is impossible with QBO. It is possible with desktop because my previous employer deposited to my checking and HSA accounts with no issue. 

How do I record HSA pretax contributions for a multi-member LLC in QBs online?  The directions I am finding are mainly for corporations with employees? Thanks!

Thank you for joining this thread, @blambert5. I'll share the steps you need to record a Health Savings Account (HSA) in QuickBooks Online (QBO).

Although you have an LLC business entity, we can set up the HSA pretax deductions as we normally do in QuickBooks. The application will automatically detect the setup of your company file, and will still report these items to the same boxes on your W-2 forms.

If you haven't set up these deductions/contributions on your employee, you can follow these steps to do so: 

1. Go to the Payroll menu, then select Employees.
2. Tap this employee, and navigate to the Deductions & contributions section. Then, select Start or Edit.
3. Select + Add deduction/contribution.
4. From the ▼ dropdown menu select:

• Deduction/contribution type: HSA plans
• Type: Pretax HSA or Taxable HSA.

1. Enter a Description(appears on the paycheck), and select how your contribution is calculated. Then enter the amount or percentage.
2. Add an Annual maximum amount.
3. When finished, select Save then Done.

Right after you run payroll, this will automatically record your employee's deductions and contributions.

QuickBooks provides a range of payroll reports that offer detailed information about your employees' gross pay, tax data, and deductions for a particular period. These reports can help you get a more comprehensive picture of your payroll records. For more details on available payroll reports and how to access them, please check out this article: Run payroll reports. 

You can always post if you have more concerns about payroll or any QuickBooks-related matters. I’m just a post away, and take care!