The practice of charging extra for a payment method over another is known as surcharging. It's not supported on Invoiced, and here's why. Most payment processors for credit cards and other electronic payment methods, including our payment processor and PayPal, explicitly prohibit surcharging in the Seller Agreement.
While the main reason that we prevent surcharging is to prevent our vendors from violating their Seller Agreement, we also think surcharging is an anti-consumer practice. Show your customer trust by letting them choose the most convenient way to pay. If possible you should build the costs of accepting online payments into your business model as opposed to tacking it on at the end of a transaction.
What if I have a large invoice? Can I control which payment methods I accept?
Yes, you are allowed to disable certain payment methods for invoices. If you have a large invoice that you only want to allow ACH payments then you can do that. When drafting any invoice you can click Options and check any payment methods you want to disable.