If you are using QuickBooks Canada and Stripe as your processor, you can now set within the Settings - Payments for Recur360 to submit to Stripe all Charge/ACH values as either United States Dollar or Canadian Dollar:
Based on the Charge Currency, this will tell Stripe what currency to charge the customer in. If you don't change the setting, United States Dollar is the default.
Currently this is a Global setting that all charges passed to stripe will be in the Charge currency. It is not on a transaction by transaction basis. If you use Stripe for Canadian processing you should setup an alternate merchant processor for United States Dollar processing so you can choose per Customer what processor you want to use.