Begin by going into File/Preferences/Payroll/Tax Liabilities:
To set up Payroll Preferences to create an invoice for tax payment through the payroll processing routine, you must add the Vendor to the Tax Liabilities screen at the bottom.
If you do this and DO NOT mark EFT at the right, it will create an invoice in AP for you to post through the normal AP Invoice Payment process (creates invoice waiting for payment). If you mark it as EFT, it will create a transaction in the General Ledger that shows the EFT payment as already paid.
Below is an example of the Vendor record used in Payroll Preferences/Tax Liabilities.
In the example above, since EFT is not marked in Preferences, when payroll is processed, an batch is created in the Accounts Payable Module.
If you Edit this batch (using the Edit pencil icon), you will see four invoices in this case, which were automatically created through the payroll system.
You may further edit each invoice and update it according to your own transaction needs. For instance, you may mark each one as pre-paid EFT here, and then post them. If you do this, it will create a GL transaction reflecting the Paid invoice for taxes. Or, if you do not mark it as EFT, you may either print the checks directly for this vendor or post it and then print them from Select items for payment.