If you’re using payroll software, it will set up direct deposit for you after you put in your information. If you’re going with your bank, you can call them or use your online portal to set up. Set up your direct deposit service: Once you’ve decided on your direct deposit provider, follow the process for setting up your direct deposit.You can work with the bank that houses your business bank account or payroll software with direct deposit functionality. Typically, you have two options for direct deposit providers. Choose a direct deposit provider: This entity will handle and house all of the information for your business and your employees.Here are the steps you will need to take. Setting up direct deposit for your employees is simple.