VEX Robotics Kit (Rant +Plea for help!)

So I have been using Arduino for the past few months, but one of my new projects requires the usage of the VEX PIC Robotics kit with MPLAB. After using Arduino I find this kit extremely non user friendly.I got over the the sparse documentation, the relatively cryptic aliases and the messy driver installation.

And when I finally had my robot working I ran into a new problem. I cannot control the VEX PWM motors from the Hardware Interrupt Service Routines! I verified that the hardware interrupts were being triggered by using printf statements to output something whenever the ISR was called. But no matter what I do I cannot change the motor speed from the ISR!

If anyone has used the VEX PIC platform please let me know how to solve this!