Hi,
You can use the Processor Expert (PEx) to customize BSP (since MQX version 3.7) that you can use in your MQX aplication. Into such BSP project, you can add PEx components you need, for examaple you can use TimerUnit_LDD component to provide PWM functionality.
There is already a example BSP project inside MQX 3.7 using Processor Expert for Kinetis TWR-K60 board insed MQX directory ...\Freescale MQX 3.7\mqx\build\cw10\bsp_twrk60n512_pe.
This project contains an example of PWM component.
Usage of this BSP in application code is demonstrated in pe_demo project in the demo directory: ...\Freescale MQX 3.7\demo\pe_demo.
I recommend to use these projects as a start otherwise you would need to configure many settings if you like to start from an empty project.
Regarding second question - yes, PEx works also in the free limited CW version.
best regards
Petr Hradsky
Processor Expert Support Team