Hi @vvicky72,

I have fully read the thread about your concern and allow me to share some information.

Right now, QuickBooks Online Payroll doesn't support yet recording the Company HSA contribution with >2% shareholder-employees. I would suggest consulting your tax adviser on how can this be done manually. 

While QuickBooks aims to find new ways to make sure that your product meets your needs, I'll be  taking note of this. I'd also encourage you to check our QuickBooks New Features to be updated of the latest product enhancements.

Let me know if you have other concerns. I'd be glad to assist you.