Hi there edwfarmscochrane,
It's important that all your transactions are correctly entered in your books so that your books are well balanced. QuickBooks Online is a program able to help you create and send invoices to your customer so you can get paid for your services. I'll be happy to share more info about QuickBooks Payments.
There isn't an ability for QuickBooks to apply a surcharge fee to your customer's end while making the payment, so it has to be deducted after when depositing the payment. I can see the benefit of having this option so you can pass this processing fee to your customers. I recommend you send feedback about this to our engineers by clicking on the Gear icon and then Feedback. The comments made in that section are taken into consideration when designing new features for QuickBooks Online.
If you have any other questions, feel free to reach out here.
