I misunderstood your question. I thought you were the contractor. Now I understand that you are the client. But the same principles apply. Use the EIN of the LLC, not his SSN. You should ask the contractor to give you a Form W-9 with the name and EIN of the LLC. You pay the gross amount. You do not withhold any taxes. Taxes are the contractor's responsibility. Make the checks payable to the LLC. The base and commissions can be combined in one check. At the end of the year issue a 1099-MISC to the LLC, using the name and EIN of the LLC. You don't even need to know the contractor's SSN. Keep in mind that he's a contractor, not an employee.
