Contractor Payroll Software: Choosing the Right Solution for Your Business Whether your business is looking to implement a new contractor payroll system or update existing software, you want to ensure that you choose the right solution for your needs. To do so, you must assess your company’s current requirements and anticipate future growth. Some offer premium tools that include automatic 1099 filing and year-end forms and compliance support for IR35 workers. It also allows you to pay contractors via direct deposit or check.