Hi there, SEConsulting.

Thanks for reaching out here for support. I'd be glad to help you record the payments in QuickBooks Online.

You'll only need to enter the remaining amount after the credit has been posted as payment against the invoice. Here's how:

1. From the Receive Payment page, select the Unapplied Payment.
2. In the Outstanding Transactions, enter the amount to be deducted from the invoice.
3. In the Amount received field, enter the remaining amount as payment to the invoice.

Please see the attached screenshot as your reference:

I'm adding this article about handling customer overpayment in QBO: Handle a customer credit or overpayment in QuickBooks Online.

Once your customer pays their invoices, here's a link on how to receive and categorize invoice payments in QuickBooks Online for the guide.

I'm always here if you have any other concerns.