When you pay your quarterly payroll taxes if you are using QBO payroll, you go to Taxes on the left side, then select Payroll Taxes at the top tab. There should be a green button there that says "Pay taxes". Use this button when paying your quarterly payroll taxes. Select from the list which of your quarterly payroll taxes you are paying (or do each, one at a time), then create payment. If your company bank account from which you pay payroll taxes is linked in Quickbooks, you can pay electronically direct to the tax agency. If not, you will not have that option, and you will enter a manual payment there. Quickbooks does the rest of the work for you to enter the payroll tax transaction if your payroll settings are set up correctly. But if you are entering a manual payment, keep in mind you will either need to physically mail your check to the agency, or pay electronically online on the agency's website. If you are entering the check in Quickbooks Online, you can enter it in either a taxes paid expense (if on cash basis) or on accounts payable for the agency you paid.
