Hi there SGoertzen,
It's important that all your transactions are entered correctly for your books to be well balanced. QuickBooks Online is a great tool able to help you keep track of expenses and sales so you know the profit of your company. I can provide some assistance with this overpayment.
One way to do this would be to first create the bill for the amount you should have been charged, and then the payment for the amount you did get charged including the overpayment. What this will do is create a credit by itself on the supplier's account, which you can then deposit to the bank account using the steps in the Deposit a supplier credit when no expense has occurred section of this article. You'll need to skip Step 1: Enter a supplier credit, as this has already been created by the payment larger than the bill.
If you have any other questions, feel free to reach out here.