Add additional code while using Mission Planner


I want to know if it is possible to use Mission Planner with the ArduPilot Mega as usual and still be able to add code to interact with the UART and or I2C? I basically want to use Mission Planner like one normally would, planning missions, setting waypoints etc. But still be able to use a camera module and save images taken with the camera to a microSD card using a breakout board.

Thank you,