I just started using this feature. I will I may not complete comprehend how it works on the back end. I have used it some and it worked ok. I have two items with issues however. I made a purchase order to purchase (1) item. Issued a credit note as payment. Later made a sales order that used this credit note as a partial payment. The sales invoice shows paid in full but the credit note is still present under credit notes and the purchase invoice
As mentioned by @Joe91 credit notes are not used to record payments. Credit notes are negative sales invoices to cancel amounts owed or adjust them. Debit notes are used in the same way for purchase invoices. You can use the Chat bot to help you on the procedure for recording payments received for sales invoices and payments made for purchase invoices.