You can issue invoices to Companies just as you would regular clients. When you opt to send an invoice in the usual ways, personnel designated to receive company invoices will do so. (And if there are no personnel set to receive invoices, the system will lovingly let you know as much when you try to send, and guide you to fix that!)
In the Client Invoicing >> Accounts listing you’ll see companies appear right alongside clients. Those clients who are associated with companies will no longer appear in the Accounts listing – they will be billed via the company, rather than individually.