I am an employee of a small company. My employer pays me a salary, plus a commission after I sell beyond my salary. He also charges me for his portion of the ss taxes he owes as my employer. I also pay my own portion. Is this legal?

No, if you are an employee he has to pay our of his money his portion of the SS taxes, you pay your 1/2 he pays his 1/2, he is also supppose to be paying unemployment taxes on you also, so if you latter leave you will be able to draw unemployment