As an employer, you are responsible for paying your staff properly. Employees should have the correct amount of taxes withheld from their checks. Employers are required to comply with the rules established by the Canada Revenue Agency. If you are a new employer, follow the steps below when setting up and running payroll in Canada. Setup Business Number: If you are an employer, you are required to submit taxes withheld from an employee’s check to the Canada Revenue Agency (CRA).