What do I do when an employee didn't come back for his check and now I'll be paying him in the next quarter?

The date on the check received by the employee is the date used to determine the proper quarter in which to report wages. When an employee doesn't pick up a payroll check until after the change in quarter (for example a check written on March 31 is not picked up by the employee until some time in April) the wages are reported according to the date on the check. 

If the employee receives the March check, then in this example, the wages would be reported in the first quarter. However, if the March check is voided and a replacement reissued in April, then the wages are properly reported in the second quarter.