Hello there, tinat.

We can receive a payment of the invoice without the wire transfer yet. Then, create a Bank deposit to link the invoice payment and wire transfer fee. This is to also avoid duplicates. 

I'll show you how: 

1. Open the existing invoice and click Receive Payment at the upper-right. 
2. In the Receive Payment page, select Undeposited Funds under the Deposit to field. 
3. Select the correct invoice and review the amount. Then, click Save and close. 

Here's how to link the payment to the wire transfer fee:

1. Go to the +New button and select Bank deposit. 
2. Select the account where the funds will be deposited. 
3. From the Select payments to add to this deposit section, select the invoice payment.
4. Under the Add funds to this deposit section, select the customer's name, the expense account used to track fees, and a negative amount of the fee.
5. The original invoice amount is being deducted with the fee. Hit Save and close. 

You can also check out this article for more details in receiving customer payments.

Get back to me if you still have other questions. I'd be glad to help you. Take care always!