communicating apm2.5 with rasberry pi

I am trying to send complex control commands from rasberry pi b+  to ArduPilot Mega(APM) 2.5, such as loitering and acquire GPS location.
i have connected both boards using USB. i was able to write a command to read 250 numbers on arduino and uploaded on APM2.5 and was able to read it.

i am not able to understand how to read compass,gps values from APM2.5 and dynamically change those gps commands via rasberry pi using 3g/4g dongle.

any help in this regard is greatly appreciated.thanks in advance

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