I'm unfamiliar with the Freshbooks API. Could a web app use Freshbooks to bill users without the user ever leaving the web app (i.e., totally behind the scenes)?
Well you will need to capture their credit card at least once. After that you can rack up charges silently. Make sure your terms of service authorize you to charge the end user at will.
To do that you can create a recurring profile through the API. Start it running today (the default) and it will immediately generate the first invoice, whose invoice_id will be returned in the Recurring.create response.
Do an Invoice.get on that id. Redirect the customer's user agent to the client_view link. They can pay the invoice and authorize autobilling from there.
After that you can Recurring.update the profile at will and every subsequent invoice will automatically be racked up in their credit card without their intervention.
