Right now, the only way to communicate with the MCU is through the MCU SDK. You can check this guide for more information on how to do this Creating applications with the MCU SDK for the Intel® Edison board | Intel® Developer Zone.
Thanks again for your kind advice. Yes, I have read that guide of Blinking an LED and wondered what that command MCU > Download is actually doing. I guess it is writing the compiled programme into some place in the storage and instructs the host OS to excute it when rebooted. Is it correct?