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 Business Center >> Invoicing >> Accounts listing you’ll see companies appear right alongside clients.  

Clients who are associated with a Company will no longer appear in the Accounts listing, unless you've selected the option to be 'Allow invoicing of individual company clients' when setting up the Company: