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If you switch mid quarter, you run the risk of both your old and new payroll services filing payroll tax returns for that quarter, both of which may be incomplete.This process can be laborious and prone to errors. If you have run any payrolls you will need to enter information into the new system pertaining to year-to-date paychecks issued and the related payroll taxes incurred and paid.Of course you could always change your payroll service at any point during the year, but this scenario presents several potential problems. You need to keep in mind all of your organization’s unique needs when selecting a payroll service, including how it interfaces with your accounting software. The need to assign certain payroll expenses to grants and contracts. The need to allocate payroll expenses by functional area (program, management & general or fundraising).Ģ. Payroll for 501(c)(3) nonprofits is further complicated by two things:ġ. As long as you need and have employees, you need to deal with payroll. The IRS is not keen on you paying people as independent contractors when they should be classified as employees. Unfortunately you can’t simply eliminate payroll. Payroll can be a complicated, never mind expensive, problem. While your fiscal year for accounting purposes may or may not be on the calendar year, your payroll system always starts out fresh on January 1. If your payroll system has been one of those problems you’d like to leave behind, the new year is a prime time to start anew. The start of a new year is fast approaching, bringing with it an opportunity to do things differently than you did them in 2017!