Invoice vs. Receipt
I most countries the law does not allow to change an invoice after has been sent. This is why only payments that have been added *before* sending an invoice are deducted from the total amount
If you like to send a Receipt after each payment: Go to the “+ Documents” section of the invoice. The Default type is a Reminder but you can can setup a Receipt in the settings icon on the bottom. Once setup, you can add payments and then send your client a Receipt.