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).
If there are other Invoices yet to be created which have the same Invoice Address as your current Invoice, you have the option to include these Invoices via the tick box on the left hand side.
Once happy with what you have selected, click CREATE INVOICE and that's it.