I just made my first successful experiment with B4R and Geekright atmega2560 board. Well, half successful since I do not know how to stop the program from running. I tried pressing reset but it restarts. I also tried removing the USB but when I put it back in it restarts again.
A micro is always running, if you don't toggle RST pin. If you take away USB you switch off power as well. So when you connect, the sequence POWER/RST restarts micro's program execution.
Ciao
Mauro