How to set up a customer to receive late fees
First thing you will need to do is set up the Customer(s) to receive the Late Charges.
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This is done Under the Customer > Property tab > More Property Information
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You can also accomplish this globally by going to Pattern>Pattern Properties and marking the customer's properties as being able to be charged late fees and updating all properties:
Charging Late Fees
In order to actually charge the late fees; go to your Quickbooks (or Invoice) Tab > Late Fee and enter in what you want to charge based on how long the invoice is overdue. You can either do a fixed fee (A flat amount you charge based on how long it has been overdue), or a percentage. You can also choose whether or not the late fees are taxable based on the tax laws of your area. Make sure you "Process" the late fees before you generate the Invoices in order for it to appear on the Invoice!