At this time, the option to create a statement charge and apply it to a specific isn’t available in QuickBooks Online (QBO). Not to worry, I have a workaround for this. You can create a credit memo if the customer is overpaid. Then, use the receive payment task for underpaid customers. Doing these processes will help you close the invoice. Also, you’ll want to add a note in the memo box that the customer is under or overpaid.
Let me show you how to create a credit memo:
On the left pane, click New + icon.
Choose Credit memo.
Enter all the needed information in every field.
Add note under Message displayed on credit memo.
Tap Save and close.
Here's how to receive a payment:
Click New + and receive payment.
Fill out the necessary info in each field.
Add note in Memo box.
Hit Save and close.
That should do it! You can check our article about handling a customer credit or over-payment.