Hello,
FreeMASTER can only communicate to one target. This is similar to multi-processor setup, you can run multiple instances of FreeMASTERs and each can may communicate with one target core. Each core shall use a different serial port or different CAN frame identifiers.
In case you use a JTAG direct memory access, you could theoretically observe both operational memory areas used by the two cores using a single FreeMASTER session - in this case you need a mechanism how to join the two map files into one and parse it with a Regular expression parser. Unfortunately, FreeMASTER has no built-in support to simplify this task.
Regards,
Michal