There are two methods to allocate a payment to a credit note: 

Method 1.

Method 2.

Both methods do not currently support allocating a part payment to a credit note.

Method 1.

This method explains how to use the Record payment form on the credit note.

You must have the 'Record payments directly from the unpaid invoice page' toggle enabled on the Settings > Configure system > Toggle features > Invoicing & expenses menu

i. Navigate to the Sales > Credit notes menu and click on the credit note number that you would like to apply a payment to.

ii. Fill out the details of the 'Record payment' form to the bottom right and hit the Pay button.

Method 2.

The second method is to import a statement and explain a payment from the statement by linking it to the credit note.

You can also create a one-off money in/ out payment on the Money > Bank accounts menu and follow steps iii - iv below.

i. Navigate to the Money > Bank accounts menu.

ii. Click on the statement that needs explaining at the bottom of the menu.

iii. Click on the appropriate payment and select the Refund tab.

iv. Select the appropriate customer and hit the Add transaction button beside the credit note that you would like to apply the payment to.