You'll be glad to know that you can enter partial invoice payments, accounts488.

You can deposited the partial payment to the Undeposited Funds account to hold it until you receive the full amount. 

Here's how to record the partial payment:

1. Click + New, then Receive Payment.
2. From the Customer drop-down, select the name of the customer.
3. From the Payment method drop-down, select the payment method.
4. From the Deposit to drop-down, select the account you put the payment into.
5. You can put the money directly into an account, like your current account, or select Undeposited funds if you need to group the payment with others.
6. From the Outstanding Transactions section, mark the checkbox for the invoice you're recording payment for.
7. In the Amount received field, enter how much money your customer paid.
8. Enter the Reference no. and Memo if needed. 
9. When you're done, click Save and close.
   
   

QuickBooks applies the partial payment to the first line item of the invoice. By design, it applies the payment to each line until the payment is used up.

To see the remaining balance for the customer:

1. Go to the Reports menu.
2. Find and open a Customer Balance Details report.
3. Select Run report.
4. Review the customer's Open balance.
   
   

If there are several payments at the bank and they're recorded as single transactions, you can post them to the Undeposited Funds account. Doing this will group those multiple records in QuickBooks. 

Learn more about this through this link: Deposit payments into the Undeposited Funds account in QuickBooks Online.

Stay in touch with me if there's anything else I can do with recording the customer's payment. I'm always around to help you.