Currently, custom payment methods can be used by a customer on the front end of site, but cannot actually apply to the order or change the order status. When creating or editing an order on the back end, admin side of things, we can tell a custom payment method to apply to the order and change the order status as if it was a credit card or other standard form of payment.
There should be an option for each custom payment method to allow it to default to being applied and/or changing order status, regardless of whether a customer or employee is creating or editing an order. This would allow a customer who places an order and pays with a custom method, such as Net 30 terms where allowed, to create an order that's marked as "Approved" instead of "Awaiting Payment." It would mean that those orders who are paid for in this fashion will show up with all other orders that are awaiting shipment because they've been paid, as opposed to being grouped with orders that aren't ready to ship because they haven't been paid for.
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