Hello there, threadgold_10.
If we've created one invoice for multiple items of your customer, we can record a separate payment for each of the items. We only have to make sure that the dates are correctly set. It'll automatically deduct the customer balance every time we record a payment.
To guide you further with this, you can check a few ways in recording the payment in QuickBooks Online. Visit these articles:
Please know that I am always to help you in case you need one. Thanks!