Hello Judy037,

Thanks for posting in the Community! 

You can use the Match or Find Match option in the For review of Banking page in QuickBooks Online. That way, you can partially apply the deposit to the customers invoice. Here's how:

1. Click on the Transactions tab or Banking tab.
2. Locate and select the bank account where the deposit was downloaded.
3. If you're not seeing a Match option on the invoice to apply the deposit, click on Find Match, and on the next page will show the possible invoice you can apply and match the deposit. 
4. Select the invoice by ticking the box next to the invoice.
5. Click on Match.

Once, you get another payment for the invoice you can use the steps above using the Match or Find match option.

You can check this link to learn more on how to Categorise and match online bank transactions in QuickBooks Online.

Post again in the Community if you have more questions. I'll be around to help you!