Please check if Allow payments to be used for automatic processing option is enabled on Top > Commerce Director > Payment Processing > General Configuration screen.
- when the option is disabled (Manual payment) - automatic assignment of unused payments on account to new documents is completely disabled. All individual settings for payments ('auto-pay' or not) are disregarded.
- when the option is enabled (Auto Payment) - automatic assignment of unused payments (credit adjustments, online payments or offline payments) with 'auto-pay' option set to new orders and invoices is enabled.
Partial payment of orders using an account positive balance is also possible. If an order total amount exceeds an account positive balance, then an order will be paid in part and a customer will be prompted about the remaining amount to pay.