How do I take into account Professional Fees that have been deducted from an Invoice Payment that we have received?

Let me help you match your bank feed transactions in QuickBooks Online(QBO), @useralhallman88.

To manage the Professional Fees, create an account for the fee and apply it as the category in the bill. Here's how:

1. From the Left panel, click the Transaction tab.
2. Select the Chart of Accounts and tap the New button.
3. Enter the Account name (e.g., Professional Fees).
4. In the Account type drop-down, select Expense.
5. Choose a Detailed type, then click Save.

The process of matching the invoice and bill with the bank transaction will include receiving payments, creating a deposit, and paying the bill. First, you need to make an invoice of $1000 and then proceed to receive payment and put it into the Undeposited Fund. Refer to the sample screenshot below:

Second, create a bank deposit and select the payment you received to match them with the bank transaction.

Here's how:

1. Click the +New under the Other column, and select the Bank Deposit.
2. Choose the account where the amount is deposited. Under Select the payments included in this deposit, mark check the invoice amount.
3. In the Add to this deposit section, choose the Supplier in the Receive from drop-down.
4. Select Accounts Payable for the Account type.
5. Enter the $300 processing fee as a negative value. This negative amount will appear as a credit that can be applied to the $300 bill you received. Once you've entered the amount, click Save.

Lastly, link the $300 bill and credit using Pay bill,  locate the bill and mark it as paid, then verify the bank transaction. It should now be marked as matched.

Additionally, you can check this article to ensure your books are accurate and balanced: Reconcile an account.

Let me know if you have other questions about matching transactions. I'm always here to provide help. Take care.