I have attempted to find information in regards to connecting an onboard computer to an APM (1.0 or 2.0), however I have found disjointed information.  I need to know if it is exactly possible to send commands to an APM via serial from a separate board (Intel Atomboard running Linux) that is on an ArduCopter?  Is it possible through the USB port?

I found some threads discussing sending commands, but most seem to be through the Base Station.  I did find commands on the wiki, but am not sure if those are also through the Base Station.  I also found some people mentioning the XBee for connection which is equivalent to what I will be doing through Serial.  Finally I found some possible avenues through ROS, but again, am unsure of what the connection is through.

In other words, I believe what I want to do is completely possible and think I have found more than enough information, but before I make a final choice, I just want to see if anyone can confirm my results.

Thanks for your help.