Great Information Here About APM and Pixhawk Flight Controllers http://copter.ardupilot.com/
Instruction Manual for RTF APM / PixHawk with TGY9X TX https://drive.google.com/file/d/0BzrvPXVuXEirOTNMMzVkcDRMR1k/view?usp=sharing
TGY9X Manual https://drive.google.com/file/d/0BzrvPXVuXEirNjJndU5nbWhQWkU/view?usp=sharing
Beginners Guide to Multirotors https://drive.google.com/file/d/0BzrvPXVuXEirdS1FQzdmVUFxaVk/view?usp=sharing
Arduino for Windows https://drive.google.com/file/d/0BzrvPXVuXEirMEJZYlVsU2hIREU/view?usp=sharing
MultiWii Config https://drive.google.com/file/d/0BzrvPXVuXEirck5IR3MzZWo4WnM/view?usp=sharing
MultiWii GUI https://drive.google.com/file/d/0BzrvPXVuXEirN0k0MFp4dEZKVms/view?usp=sharing
CC3D Open Pilot https://drive.google.com/file/d/0BzrvPXVuXEirUHYtdFZhLXZPU2c/view?usp=sharing
Mission Planner https://drive.google.com/file/d/0BzrvPXVuXEirSGFxemQwUXFHd0U/view?usp=sharing
APM Planner https://drive.google.com/file/d/0BzrvPXVuXEirM25xMm13Vm9vNTA/view?usp=sharing
Here are some resources for mission planning/surveying and info on the features of the flight controller.
These are guides/examples and every mission/survey may have to be tweaked to your specific conditions.
Ardupilot Website
http://ardupilot.org/copter/index.html
Copter Mission Command List
http://ardupilot.org/copter/docs/mission-command-list.html
Mission Planning
http://ardupilot.org/copter/docs/common-mission-planning.html
Mission Planner Part 1 - Introduction
http://youtube.com/watch?v=rui2Trps2yc
Mission Planner Part 2 - Advanced Flight Planning
http://youtube.com/watch?v=4rrQNlghpO4
Survey with Mission Planner and Ardupilot
http://youtube.com/watch?v=i0oL5wek-c4
3d Mapping Overview
http://ardupilot.org/copter/docs/common-3d-mapping.html
Camera Control and Auto Missions in Mission Planner
http://ardupilot.org/copter/docs/common-camera-control-and-auto-missions-in-mission-planner.html