How To Use Manual Payroll in QuickBooks Many small businesses have a payroll consisting of only one or two people, and are happy to continue preparing payroll manually, but would like to know what payroll tracking is possible in QuickBooks without purchasing the tax table updates every year. QuickBooks will let you enter the withholding amounts manually. Effective with QuickBooks 2007 Release 4 and QuickBooks 2006 Release 9 QuickBooks has removed access to the manual tax forms- 941 & W2.