Invoices are created as a result of processing Program Registrations, Facility Reservations (that require payment), Membership Enrollments, POS transactions and Drop-In Program Check-ins (that require payment). Once you click on the Checkout button from the Shopping Cart you will be directed to the Pending Invoice page. Clicking Create Invoice will create the invoice and then present you with the various Payment Options.
After the payment is processed, the invoice is available. See What is the Invoice List?