Just want to know what I should do. I worked for a company that paid me a salary plus commission. The salary was done through Paychex so I go a W2 for that but did not get anything else. Can or should they give me a 1099 for the commission? If I claim it won't I have to pay self employment tax? And is that legal for the employer to not pay matching taxes for an employee? Thanks in advance!!

Many companies do this. Now you must report 1099-misc on schedule C or C-EZ and pay SE tax at 15.3% (which is your share as well as employee's share of FICA taxes). Thus you pay about 7.5% more than a W2 employee.

But there are many advantages of getting 1099-misc. You can directly deduct your business related expenses on schedule C instead of taking itemized deduction.
Read: Your U.S. Tax Return: W2 vs 1099-Misc: Employee vs Independent Contractor. (http://taxipay.blogspot.com/2008/03/w2-or-1099-employee-or-independent.html)

Good answer