Yes, you can can reconcile payments between invoices and credit notes under Supplier invoice - Manual Payments.

 Follow these steps:

• Select the checkboxes for both invoices (credit note and supplier invoice);
• Change the Payment Date (if necessary);
• Set the same amount to the normal supplier invoice as it is in the credit note (if the normal invoice has a bigger amount than the credit note);
• Choose the Payment Method which is suitable for you
• and Post

Proceed in the same manner to for Customer invoices and credit notes under: Invoicing - Payments.