When an invoice is set up and the Enable Auto Pay box is checked the payment will be taken on the due date (if a single transaction) or on the day/date chosen in the Recurrence dialog.
Setting Up Auto Payments
The 'Create Invoice' screen now includes a 'Schedule for Auto Payment' option. Once selected, the user will be prompted to either use a saved card (or enter a new card) to associate a payment source with the auto Payment. "Set Recurrence" functionality remains unchanged- the whole series of invoices will have autopay enabled on them.

Note that if the due date is the same day you are creating the series, you will need to pay the first invoice manually- auto billing will only start on invoices due the next day or later.