Hi Daniel,
Please have a look at the following demo:
C:\Freescale\Freescale_MQX_4_0_2\demo\pe_demo
It uses a Processor Expert component for the PWM operation.
All MQX BSP's are PE capable. So have a look at the following PDF to see how to enable the PE in the BSP:
C:\Freescale\Freescale_MQX_4_0_2_GA\doc\tools\cw\Howto_SetupKinetisClock_UsingPE.pdf
Then when you look through the pe_demo source code in the comments, it explains how the MQX application can access the PE component(s) that are added into the BSP.
Hope this helps.
Regards,
David