If a customer pays an invoice emailed to them, we pay a 3.5% + $.30 for the payment?  That's considered a "card on file"?

As stated above the fee for invocis is 2.9% plus $0.30.  This is if the customer just enters their card information.  If they have their card information saved then it is 3.5% plus $0.15. Customers can only save there card on file if you allow it when you send them an invoice.  

Thanks!  That clears it up.

From these numbers it charges MORE if you have their card saved, which you would think would be less expensive and easier.... So why would anyone ever let their customers use a card saved on file if it charges us as the business more in fees than if we just have them reenter their information every time?

Hello @Baker27, Card on File is geared towards businesses with recurring memberships.

For example a gym might opt for Card on File, so members don't forget to pay their dues on time. It also reduces the amount of overdue invoices.