1. to exit a loop, use break, e.g.
if( employeeName.toLowerCase().equals("stop"))
break;
2.
while(hourlyRate < 0)
and
while(hoursWorked < 0)
are always true when they are given positive value the previous time.
use do...while instead, e.g.
do {
System.out.print("Enter a positive hourly rate: $");
hourlyRate = input.nextDouble();
} while (hourlyRate < 0)