Partial payments credit card fees

Hi there, @JessB. 

Glad to know that you already have an expense account for your credit card fees. 

To make sure that the payment amount showing on the bank feeds matches the deposit amount in QuickBooks Online, you'll need to enter the credit card fees in the register, then record the fee as a negative amount on the Bank Deposits screen. 

I'd suggest you undo your matching activity first so the transaction will go back to the For Review tab. Then, match the transactions after recording the credit card fees. Here's how: 

1. Go to the Reviewed tab on the Banking page. 
2. Find the transaction, then click Undo in the Action column. 

Here's how to enter the credit card fees in the register:

1. Click the + New tab on the left menu. 
2. Under the Customers, choose Receive Payments. 
3. Enter all the payment information.
4. Select the checkbox next to the invoice you would like the payment to be applied to.
5. Select Undeposited funds in the Deposit to account.
6. Choose Save to record the transaction.

Once done, record the fee as a negative amount in the Bank Deposit, here's how:

1. Go to the + New tab on the left menu. 
2. Under Other, choose Bank Deposits. You should see the payment you entered in the Select Existing Payments section.
3. Put a checkmark to select the payment you want to deposit.
4. From the Add other funds to this deposit section, enter the amount of the fee charged to you by the credit card company as a negative amount.
5. From the Account section, click the field and select the Expense account in the drop-down list to track your credit card fees. 
6. Verify that the deposit amount is correct.
7. Click Save when done.

You can now match your bank feeds transactions with your payments. For more information, check out this help article: Enter a bank service fee while using a third-party merchant service. It helps you learn about how to record service charge fees in Quickbooks. 

Let me know if you have any more questions. I'm always delighted to help.