Thanks for joining in this conversation, @Mara. There's no difference in recording transactions in QuickBooks Online. I have a step-by-step guide in recording the processing fee to make sure it matches your bank feeds. 

For instance, you have a $50 invoice and a $2 processing fee, which gives you a $48 net bank deposit. You'll need to record an invoice showing the full amount first, then receive the payment with the same amount as the invoice.

Step 1: Create a customer invoice

1. Click the +New menu.
2. Select Invoice, then enter the exact amount ($50) to be invoiced.
3. Click Save. See screenshot below: 

Step 2: Receive the payment

1. While you're on the invoice page, click the Receive Payment button.
2. Choose Undeposited Funds in the Deposit to field.
3. Click Save and close. See screenshot attached:

Then, deduct the processing fees in the Bank deposit window. Don't enter zero to avoid getting error when you deposit the payment. Instead, enter a negative fee amount. Here's how: 

1. Go back to the +New menu, then select Bank Deposit.
2. Mark the invoice payment you received previously from the Select the payments included in this deposit section.
3. Expand the Add funds to this deposit section to add a new line item.
4. In the Received From column, enter the processing fee as a vendor, then add an expense account for the fee in the Account column.
5. In the Amount field, enter a negative fee amount (-$2). 
6. Ensure that the deposit matches the net bank deposit amount.
7. Click Save and close. See screenshot below: 

For future reference, read through this article: Add and match downloaded banking transactions. It helps you learn about how to review your bank feeds transactions to make sure they're added to your books. 

Feel free to message again if you need additional assistance. We're always delighted to help you more.