Allow me to share some information about the flows of payments and deposits in QuickBooks Online, @jd34mx.

If the invoice is paid through Merchant Service (QuickBooks Payments), the payment will be posted to the Undeposited Funds temporarily, and not directly to your bank account where the merchant deposits the money.

The Undeposited Funds is an internal account that QuickBooks uses to hold payments. It's designed to work with the receive payments and bank deposit features to complete the invoicing process.

This means if your bank recorded a single deposit, you should do the same in QuickBooks. You'll want to create a Bank Deposit then add the fees from there. This way, it will match your actual bank. Here’s how:

1. Select the +New tab.
2. Click Bank deposit under Other.
3. Enter the account and select those payments.
4. Click Add funds to this deposit.
5. Add the fees as a negative amount. 
6. Select Save and close.
   

You can read these articles for more insight about the process:

• What are Bank Deposits in QuickBooks?
• Deposit payments into the Undeposited Funds account in QuickBooks Online

I’ve also added this reference to guide you thoroughly on how to match, add, or view multiple matches: Categorize and match the online bank transactions in QuickBooks Online.

Don’t hesitate to get back on this page if you have other questions. We’re always here to lend a hand. Keep safe.