Once a job is booked, you can create new orders for that existing client. Note that you can only create new orders for "booked shoots." Orders are associated with booked shoots, not individual clients. So you need to have a "booked shoot" in order to create an order/invoice.
Click "Create An Order" under the Billing & Legal section of the shoot.
You are directed to a screen that looks similar to the one when you create a proposal. You can choose a standard package (or build a custom one), and then modify the settings (taxes, discounts, payment collection, etc) for this order. You can also choose which customer to bill.
When you finalize the order you can send your client an email with a link to the invoice. They can also pay the invoice in their client area.
In the Billing & Legal section of the shoot in the photographer view, you now have a new order which has its own settings, payment method, contracts, payments, etc.