In the case you have captured the payment in the Payment Gateway instead in the Order Manager you have capability to process the order and mark it as shipped or picked up.
Please follow these steps:
- Select the order
- Click on "Process Stuck Order"
- Select the Amount (Amount as Shown or Custom Amount)
- Select from the drop down where the funds were captured
- Check the acknowledgment check-box
- Click the "Confirm" button
Done.
The order has been processed with in the system and marked either as "Order shipped" or "Picked up"