We have an employee coming to work here in the US on a H1-B visa, how would we tax the employee's wages?

The type of Visa an individual holds will dictate whether or not the individual is exempt from Social Security or Medicare taxes. For H-Visa holders, they are not exempt from Social Security or Medicare taxes so the employer would need to withhold these taxes as well as pay the employer's share. He would also be subject to income taxes.