Hi Lance,
MCAT interface communicates with the MCU using UART. It will depend on how are you communicating to the Freemaster interface from your project. Maybe it would be easier if you use the software given as a starting point and modify it according to your custom board needs.
Unfortunately, we have no guide describing procedure when using custom board because this will vary on each design.
If you have any specific question please let me know.
Best regards,
Felipe