Thank you for the additional information, MichaelDougherty.

We can add the Stripe fee as we deposit the invoice payments. Here's how:

1. Open the invoice and click the Receive payment button.
2. Enter the Payment date and the Payment method.
3. Select Undeposited Funds in the Deposit to field.
4. Click Save and close.
5. Click the + New button and select Bank deposit.
6. Select the bank account in the Account field and enter the Date.
7. Under the Select the payments included in this deposit section, mark the invoice payment.
8. Go to the Add funds to this deposit section, and select the bank fee account in the ACCOUNT column.
9. Enter the bank fee as a negative amount and click Save and new.

Then, you can create an expense account for the processing fee to resolve the difference between the invoice and the payment when matching transactions from your bank feeds. Here's how:

1. Click on Accounting at the left panel, select Chart of Accounts.
2. Select New.
3. In the Account dialog, create an Expense account for Stripe Fees, and add the name.
4. Click Save.

Then, when matching the transactions:

1. Click on Banking at the left panel.
2. Select the appropriate bank account from the list.
3. Locate and select the transaction in the For Review tab, then select Find Match.
4. In the Match transactions window, select the checkbox of the appropriate Invoice.
5. Select Resolve Difference to open the Add resolving transactions field.
6. Select Add new transaction.
7. From the drop-down list in the Category field, select the Bank Fees (processing fee) expense account you created.
8. Enter the negative Amount of the bank/processing fee.
9. Click Save.

Learn more about matching transactions in QBO: Match and categorize your downloaded bank transactions.

Let me know if you have other questions.