How do you set up net payroll payments so Quickbooks add on the tax due?

Hello there, @tricia16.

The Payroll function in the system is not linked to the Vat/tax return.  Income taxes are for payroll transactions, and sales taxes are included in the VAT section. Therefore, these taxes are two separate submissions.

When running payroll in QuickBooks Online, the net payment will be posted automatically since it creates a payroll journal. That said, you'll need to report real-time information (RTI) to HMRC, informing then about the net payments.

To give you more insights on how this process work, please see these links:

• Turn on RTI reporting to HMRC
• Submit FPS to HMRC in QuickBooks Online Standard Payroll (UK)

Let me know if you have any other questions. I'll be around to provide further assistance. Have a good night!