In Help Desk version 3.x, companies can be created, and users added to companies.
Visit Administration > Users, then click the "Companies" tab:
Provide a name for the company, an optional SLA Plan, and allow privileges or auto-join to occur.
Once a company is added, you can apply public users to that company:
When public users of a particular company submit support tickets, the ticket will automatically inherit that company information:
Billing entries will also be auto-populated with that user and company information:
