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Auto-pay is one of the options you will see when creating Scheduled transactions. Please note that you will only see this option if the account you've picked for your Scheduled transaction is not connected to Online Banking.
Auto-pay should not be confused with auto-skip.
If you have some transactions that occur regularly, with same amount each time (e.g. rent or salary), you might want to automate those transactions so they get posted into your Account register automatically as they become due.
In order to do this, simply enable "auto-pay" when creating Scheduled transactions. This will cause that particular Scheduled transaction to get posted to your Account register automatically, if MoneyWiz is running or launched while the transaction became overdue (the due date of the transaction arrived).