Thank you for the detailed information about your concern for recording an overcharge in QuickBooks Online, @myhbs.

It's fine to add a negative line item on your invoice to reduce the amount that has been overcharged from your fees. This way, you'll be able to create a single transaction for your customer. Just make sure to enter a description on the line item indicating the reason behind the negative figure.

Please see the sample snip below on what your transaction will look like: 

On the other hand, if you're going to process a credit memo, it would be a separate transaction. The good thing about this is that it is specific because you'll be able to select the exact date of the overcharge. 

You can choose any of these options as they have the same effect in QuickBooks.

Know that you can always get back to me if there's anything else that you need. I'll be here for you. Wishing you well!