Once an order has been finalized you can create payments.
Note
You must create an invoice in order to make payments.
There are two ways to make payments. You can either make a partial payment or a full payment.
To create a partial payment click on the green dropdown box at the corner on your invoice tab and select pay:

To make a full payment click on the 'Pay All' button on your Payments tab:

Your payments have now been made.