MAVLink messages from different source

Hello everybody
I am building a drone that can track objects
It is based on Raspberry Pi2 and Navio+ board
My idea is to develop an application (that will run on the Raspberry Pi2) that captures images by means of a RaspiCam, detect objects and send MAVLink MAV_CMD_CONDITION_YAW command to ArduCopter (that runs on the same Raspberry Pi2 board).
So my question is: is it possible to send MAVLink commands from both the GCS and my custom application?

Thanks in advance and happy ew year!

Yes