Do I have to pay paypal per transaction on top of the monthly fee to you?
Yes, all payment processors have their transaction fee. We only charge a monthly fee for our service.
I presume that there's a transaction fee associated with accepting payments from PayPal and others that's entirely separate from your cart and reporting?
Yes, although Google Checkout is free till end of the week and then if you spend any money on Adwords, you can accept 10 times that amount without any transaction fee. There is no fee with TrialPay.
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