I've got some steps we can perform to apply for the customer's credit when matching the downloaded transactions, debi8.

For customer credit or overpayment, we can use the credit toward an invoice, refund the customer, or enter the overpayment as a tip in QuickBooks Online (QBO). Just follow the steps and details in Handle a customer credit or overpayment in QuickBooks Online article to keep track of the credits in your account.

Then, deposit the customer's payments in your account. Let me show you how: 

1. Click the +New Plus icon. 
2. Select Bank Deposit.
3. Choose the account you want to deposit the payment.
4. Tick the box beside the customer's payment.
5. Press Save and close.

Once done, match the payment transaction that is already downloaded on the Banking page. Here's how:

1. Go to the Banking menu and select the bank where your customer's payment has been deposited.
2. Find the transaction with the correct details. QBO will automatically detect the transactions that matched with the downloaded ones from the bank. A green mark will show on the transaction.
3. Tick the transaction and verify the details.
4. Press the Match button.

If the amounts are different, just locate additional matched transactions or select Resolve Difference. This opens the Add resolving transactions fields wherein we can include the Category and Amount of a resolving transaction until the difference equals zero. We can also use the Add new transaction button to add multiple resolving transactions. Just review the process in the Categorize and match online bank transactions in QuickBooks Online article. 

When you're ready to assess your business financials, you can reconcile your bank account in QBO. Feel free to visit our Banking page fr more insights about managing your bank transactions.

I'd like to know how you get on after trying the steps, as I want to ensure this is resolved for you. Just reply to this post and I'll get back to you. You have a good one.