You can select a project-level class in the Projects screen > General > Billing Options to be used for time and expense entries logged against it, as well as the related invoices. The relationship between a class and a project is one-to-one (a project can be assigned to one class only). You need to assign a class to the projects before creating invoices and prior to synchronization with your accounting software, say QuickBooks. You can set the class for multiple projects using Actions > Batch Update. Select the projects and then on the Batch Update screen, select Class and enter a new value and click Save. It will be applied to all the selected projects and their future invoices.
You cannot set a class for existing invoices.