How best to pay those who need checks for two different types of work?

Q: “I have a client with several employees receiving two payroll checks. The first is for a normal 40-hour week at one rate of pay. The second is for a different job, at the same company, at a different hourly rate. The second work hours are from 2 to 15 hours after the regular 40-hour workweek. In most cases the second job’s hourly pay is more than the first. This is in New York City. Is there any violation?” – Kenneth, New York