Using Mission Planner with Raspberry Pi as a main controller for Drone

I am working on Raspberry Pi 2 Model B as a main controller, 10DOF (L3G4200D_ADXL345_HMC5883L_BMP085 )IMU , and neo cn-06 GPS module.
I’m wondering if I can use an open-source GCS like Mission Planner with my flying system or it is just done for pre- full defined system like Ardupilot.

Mission planner talks mavlink. with customozation for ardupilot. Mission planner will talk to anything that is also talking mavlink.