If you're employing manual processes. So you don't have to worry about providing your login information online because QuickBooks POS uses a secure mechanism for all of its activities. You may use direct deposit for both employees and merchants in QuickBooks (this service may cost extra depending on which QuickBooks payroll plan you choose). Direct Deposit Forms QuickBooks, Direct Deposit Authorization form QuickBooks, Set up Direct Deposit in QuickBooks Desktop We'll start by going through how to set up direct deposit in QuickBooks. Then we'll go over how to use deposits to pay users.