Thank-you for joining in on this thread and being a member of the QuickBooks family @heavyduty!
Using our Payments add-on is a fantastic way to receive your customer's credit card payments towards their invoices. To answer your question - yes. If you receive a credit card payment from your customer using QuickBooks Online Payments Canada, you'll be charged a 2.9% + $0.25 fee. This fee is charged on every transaction you process using Payments. A $40,000 payment is no different than a $50 payment in that you're still charged the same 2.9% + $0.25. The Fee Disclosure is broken down for you in the Intuit Payments Merchant Agreement so I encourage you to review it for more information on this.
I'm here if you need any further clarification!