I think that you should file form 8919 with code H. This form lets you pay the SS and Medicare taxes that you owe (just the employee half). I also thinks it tips off the IRS to audit your employer. If you are doing the work of an employee you are not responsible for the employer half of these taxes. If you are doing some work as an employee and some work as a contractor then he might be doing it right, but probably not. If anything he should also give you a 1099-MISC.
