You should tell the company that you will have to raise your rates to cover the added expenses and work. It won't be much added to an hourly rate (assuming that's how you charge). But be sure to add in the fees, your time to cover annual reports and other expenses, and the cost of an accountant just in case.
Also, make sure your rates already include burdens such as all your fringe, insurance, OH, etc. You're a company too, and the money that your boss'company saves by not having to pay you benefits means that YOUR company has to pick up all of those costs..