For orders with a balance, such as those with cheque or other manual payments, or recurring (monthly, quarterly, etc.), you can manually apply a payment.
Add a payment
Navigate to the order, and click the "Add payment" button located in the Payments area.
The payment form will open allowing you to choose between the payment options in your configuration. In this form you can choose to make a partial or full payment. When completed, click "Add payment."
The payment will now appear in the Payments area of the order. In the case of a declined credit card, the declined transaction would appear here as well for your information.
The Outstanding Balance of the order will automatically be decreased by the amount of the payment.