Hello there, customerservice-3.

I'll provide insights into how customer payment works using the Merchant service. I'll also ensure you can handle the charge taken from the payment and match your entries in the program seamlessly.

When you use a merchant service to take credit card payments, the credit card company deducts bank service fees from the payment similar to what you experienced. As a result, the amount displayed on the bank record doesn't match the deposit amount in QBO.

I recommend entering the credit card fee directly into the register so that the balance matches the bank statement. You'll then need to record a bank service charge as a negative amount on the Bank Deposits screen.

Here's how:

1. Choose + New and Receive Payments. Then, enter all the payment information.
2. Select the checkbox next to the invoice you would like the payment to be applied to.
3. Choose Undeposited funds as the deposit to the account.
4. Click Save and close to record the entry.
5. Click the + New button again.
6. Select Bank Deposits. You should see the payment you entered in the Select Existing Payments section at the top.
7. Place a checkmark to select the payment you want to deposit.
8. In the Add other funds to this deposit section, enter the amount of the bank service fee charged to you by the credit card company as a negative amount.
9. From the Account section, select the Expense account you usually use in tracking bank fees.
10. Double-check that the deposit amount is correct.
11. Click Save and close.

Once done, you can match the downloaded payment to the created bank deposit with the fee. 

In case you need guidelines on how to reconcile your accounts to avoid discrepancies, you can read this article: Reconcile an account in QuickBooks Online.

If you have any clarifications about customer payment with processing fee, you can add them below. I'll get back to you as soon as I can, customerservice-3. Have a good day!