Once you create an invoice in Payments > Invoices, you will see a button that says "process payment".

If you need to process a one time payment, you will click process payment. A screen will pop up that allows you to enter the payment amount, and the payment method. Enter the credit card number or ACH and then click Process Payment at the bottom.

After this is done, you can go to the Payment tab and it will show the payment you just processed. The top will show total fees, total received, and total still owed.