Instructions and Setup Manuals/Videos.

Great Information Here About APM and Pixhawk Flight Controllers

Instruction Manual for RTF APM / PixHawk with TGY9X TX

TGY9X Manual

Beginners Guide to Multirotors 

Arduino for Windows

MultiWii Config

MultiWii GUI

CC3D Open Pilot

Mission Planner

APM Planner

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

Copter Mission Command List

Mission Planning

Mission Planner Part 1 - Introduction

Mission Planner Part 2 - Advanced Flight Planning

Survey with Mission Planner and Ardupilot

3d Mapping Overview

Camera Control and Auto Missions in Mission Planner