Hi there, @2dogs.

You can record the processing fees in two ways. I'm here to share them with you.

First, you can add an expense amount when recording a payment/bank deposit.

Here's how:

1. Go to the (+) New icon, then select Bank deposit.
2. Select the payment you want to deposit.
3. Add the processing fees in a negative amount under the Add funds to this deposit section.
4. Save the transaction.

The second option is to add the fees to the customer's invoice. You can add the fee to the invoice if you want your customers to pay the processing amount. Before that, you can use a service or a non-inventory item to record the fee. 

1. Go to the (+) New icon, then select Invoice.
2. Fill in the information (date, item, amount, and others).
3. On the second line, choose the item created, then enter the fee amount.
4. Save the transaction.

You can also open this link to learn more about accepting credit or debit card payments in QuickBooks Online.

Moreover, here's how you can choose where to record payments and processing fees for QuickBooks Payments.

If you have any other questions about processing invoices online, please let me know by adding a comment below. I'm always here to help. Have a good one!