Paychex Flex Select is the company’s most popular payroll plan.The company notes that processing W-2s and 1099s may require an added fee. It includes calculating, filing and paying your business’s taxes, and distributing payments to employees by paper check, direct deposit, or pay card, as well as tip disbursement for eligible workers. Paychex Flex Essentials meets the needs of firms with 1 to 19 employees and costs $39 a month plus $5 per employee.