Enter Receive Payment, apply it to any existing unpaid in...
Enter Receive Payment, apply it to any existing unpaid invoices as appropriate. QB will ask you what you want to do with any unapplied amount - choose "Leave the credit to be used later".
After you create a new invoice for the same customer, go again to Receive Payment. Enter the payment amount. If you have selected the Preference - Payments to "Automatically apply payments", QB will usually apply it to the oldest invoice first, then the next, etc. Again there may be an unapplied amount. You can change the way the payment is applied by "de-selecting" (click to clear the checkmark) an invoice and selecting a different invoice, and/or by changing the amount in the Payment column.
If you do not apply payments automatically, then click to select an invoice (anywhere on the invoice line but NOT in the checkmark column), then click Discounts and Credits in the icons at the top of the Payment window.