Hi there CGLog,
Making sure to enter transactions correctly is an important part of your bookkeeping. QuickBooks Online is a great tool to help you manage your receivables and keep track of unpaid invoices. I can provide some assistance regarding this.
One way to trach this would be to use a deposit with fees in order to record the amount deducted by the bank. In order to accomplish this. When creating the Payment on the invoice, instead of sending it directly to your bank account, choose the Undeposited Funds account in the Deposit to the field. Once that is created, click on the +New button in the top left of your screen, then select Deposit. Select the invoice payment within the list of transactions, then you can add the fees in the Add Funds to this deposit section as a negative amount. Here's an article that provides more details on how to create a bank deposit. The information for the fees would be located in the Include bank or processing fees section.
If you have any more questions, feel free to reach out here.
