Yes - there are two semi-independent concepts going on. But you still have to download the program to the Cortex.
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While Robot C is going, the communication from the Joystick or Cortex to the PC uses Robot C specific messaging versus characters streaming across. Probably some compression techniques to get more data to the PC in less time.
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Don’t use the Robot C write debug stream line and write messages yourself out the serial port to your PC. This can be run any time the program runs and not while robot C is hooked up.
jpearman explanation here with a link to the code he wrote:
If you want to go further with option 2, you can hook that serial connection to an Arduino that is storing the serial data to an SD card or you could use an XBee to communicate back to the PC. Several other choices are available here but involve make your own as well.
Or be semi-lazy like me and write to the debug stream lines and copy/paste into Excel or Open Office to make pretty graphs. This leads to re-downloading programs to the Cortex every time you set a variable to a new value (like the proportional constant in a PID tuning exercise to find the magic Ku value)