All Orders with a Payment Method of either On Account or Other, will drop into Awaiting Invoicing (see here for fuller explanation).
Go to Invoice Module.
All un-invoiced Order will be displayed in date order in Awaiting Invoice.
You can filter the list using the fields above. You may want to find all Orders for a particular Customer, a defined date range, a Customer Analysis field you have created (or a particular site - if you use the multi-site version).
Click on INVOICE against the Order to be Invoiced - then you are able to amend certain of the Order fields - for example, you may need to add a Purchase Order reference number or amend the Customer Name slightly).
Once happy, click CREATE INVOICE and that's it.
For information on Multi-Order Invoices, click here.