Timer issue in Arduino mega

Hello folks,

Right now I'm working on stepper motors and using PWM.h library I'm giving different frequencies for both stepper motor. Earlier I'm using Arduino UNO but now I'm using Arduino Mega. When I'm working with UNO I'm using Timer 1 and 2. But now I'm trying to running these motors using Arduino mega and now I'm facing an issue with this...like only one timer is working at a time. So only one motor is working..