I am not exactly sure what you mean by keeping the companies separate however adding a new email domain is fairly easy.
Go to Exchange System Mananger / Recepients / Recepient Policies.
There will be at least a “Default Policy” You will probably want to create a new policy so that you can assign specific users to the policy. YOu assign users by clicking modify at the General tab. When you have created the policy you then add a new SMTP address matching the new domain.
These are the basics. Someone else may need to help you with more detailed information.