If you ordered an RC transmitter with your RTF aircraft, this process has already been completed for you.
Pixhawk is compatible with PPM RC receivers, Futaba S.Bus receivers, and Spektrum DSM,DSM2, and DSM-X Satellite receivers. For traditional single-wire-per-channel (PWM) receivers, a PPM encoder can be used to convert the receiver outputs to PPM. For a list of RC systems compatible with Pixhawk, click here.
For Spektrum Satellite receivers, connect to the SPKT/DSM port.
For PWM receivers with a PPM encoder (purchase from store.3dr.com), connect the 10-wire and three-wire cables to the PPM encoder (1), connect the 10-wire cable to your PWM receiver by channel (2), and connect the three-wire cable to the Pixhawk RC pins (3).
Connect Pixhawk to your computer using the micro-USB cable.
To calibrate your RC system, open a ground-station application. For APM Planner 2, follow the instructions here to connect Pixhawk. For Mission Planner, select the available COM port in the top-right corner, set the rate to 115200, and select connect. Then follow the instructions here to perform RC calibration and the instructions here to assign flight modes.